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Cavendish moved in front first but Kittel gained ground and just beat him to the line to earn his second stage win in three days, and third of this race.
"As we say in Germany, good things come in three," the 25-year-old Kittel said.
"It was close. I don't know what to say.
"It was a real sprint today, that's why I'm so happy."
It has been a nervy Tour so far and about 20 riders were caught in a crash near the end, with some stuck under the bikes of others as wheels and frames jutted out at all angles.
"It's always like that at the end before a sprint," Froome said.
"It's scary for everyone."
Froome still leads Alejandro Valverde by 3 minutes, 25 seconds and is 3:54 ahead of two-time former champion Alberto Contador.
Cavendish, the Tour's best sprinter two years ago, has had a frustrating race so far.
The British sprinter looked well set to clinch his 25th career stage win of the Tour as his Omega Pharma QuickStep teammate Gert Steegmans got him in a great position to attack.
But Cavendish did not have the legs to hold on and Kittel beat him by half a wheel's length.
"I can go back and look over it but he was just faster," Cavendish said.
Peter Sagan finished third and still has a comfortable lead as he bids to win the sprinters' green jersey contest.
Sagan has 307 points, and leads Cavendish by 96 points. Greipel is in third place and Kittel is fourth, but both are more than 100 points adrift of Sagan.
Keen to keep their riders near the front of the main pack and limit the risk of them being caught in crashes, Froome's Sky and Contador's Saxo-Tinkoff squads took turns pushing from the front.
"That is the best position to be in because there are crashes everywhere," Froome said.
"I did hear the crash behind me."
Saxo-Tinkoff tried to pull away with about five kilometres left, but Ian Stannard helped Froome catch them.
German sprinter Andre Greipel and Norwegian Edvald Boasson Hagen were among the 20-odd riders who were caught in the latest big crash of the Tour, and moments later Froome survived a delicate moment when he appeared to be nudged by Tom Veelers.
Boasson Hagen was clutching his shoulder when he got back up.
"He's being examined by the doctor at the moment, but I don't think he's broken his collarbone," Sky team manager Dave Brailsford said.
"He is in a lot of pain, but we hope he'll be able to continue."
Froome said his teammate is "a huge part of the team, and I hope he's OK."
A five-man breakaway surged ahead very early on.
The group consisted of Spanish veteran Juan Antonio Flecha, Italians Francesco Gavazzi and Manuele Mori and Frenchmen Anthony Delaplace and Romain Sicard, and they built up a lead of about nine minutes after about an hour of racing.
The peloton rolled through vineyards and alongside the Chinon forest on a 218km route from Figures to Tours in the Loire valley, a picturesque region dotted with imposing French chateaux such as the spiral-towered Chateau d'Usse, which dates from the 11th century, and the 16th century Chateau d'Azay-le-Rideau, which rests on the water.
Amid the sightseeing, there were still some minor crashes before the big one late on.
French riders Alexandre Geniez and Blel Kadri both tumbled and Latvian Gatis Smukulis even managed to fall off his bike in the feed zone.
Canadian Svein Tuft went too fast around a roundabout and slid across the road. They all got back up and continued.
Andy Schleck, the 2010 Tour winner who had a disappointing time trial on Wednesday — finishing nearly five minutes behind the winner Tony Martin — had to change his bike after a puncture and scampered back to rejoin the main pack.
Sicard dropped off the pace with a little under 50km to go, leaving only four in the lead group.
No breakaway has managed to go all the way yet on this Tour, because the peloton has been riding so aggressively, and the 35-year-old Flecha was the last rider to be caught, about six kilometres from the end.
Froome finished just behind Martin in Wednesday's time trial to extend his lead.
Standings from the 12th stage of Tour de France, a 218km ride from Fougres to Tours(average: 45,1 km/h):
1. Marcel Kittel (GER/ARG) 4h49min 49sec
2. Mark Cavendish (GBR/OPQ) at 0:00.
3. Peter Sagan (SVK/CAN) 0:00.
4. Alexander Kristoff (NOR/KAT) 0:00.
5. Roberto Ferrari (ITA/LAM) 0:00.
6. Daryl Impey (RSA/ORI) 0:00.
7. Jos Joaquin Rojas (ESP/MOV) 0:00.
8. Yohann Gene (FRA/EUC) 0:00.
9. Juan Jos Lobato (ESP/EUS) 0:00.
10. Samuel Dumoulin (FRA/ALM) 0:00.
11. Serguey Lagutin (UZB/VAC) 0:00.
12. Gert Steegmans (BEL/OPQ) 0:00.
13. Julien Simon (FRA/SOJ) 0:00.
14. Chris Froome (GBR/SKY) 0:00.
15. Egoitz Garca (ESP/COF) 0:00.
16. Michal Kwiatkowski (POL/OPQ) 0:00.
17. Nairo Quintana (COL/MOV) 0:00.
18. Alejandro Valverde (ESP/MOV) 0:00.
19. Roman Kreuziger (CZE/SAX) 0:00.
20. Cadel Evans (AUS/BMC) 0:00.
21. Matteo Trentin (ITA/OPQ) 0:00.
22. Nicolas Roche (IRL/SAX) 0:00.
23. Andrew Talansky (USA/GRM) 0:00.
24. Alberto Contador (ESP/SAX) 0:00.
25. Koen de Kort (NED/ARG) 0:00.
26. Tom Dumoulin (NED/ARG) 0:00.
27. Elia Favilli (ITA/LAM) 0:00.
28. Ian Stannard (GBR/SKY) 0:00.
29. Fabio Sabatini (ITA/CAN) 0:00.
30. Roy Curvers (NED/ARG) 0:00.
31. John Degenkolb (GER/ARG) 0:00.
32. Tony Martin (GER/OPQ) 0:00.
33. Andr Greipel (GER/LTB) 0:00.
34. Alexandre Geniez (FRA/FDJ) 0:00.
35. Arthur Vichot (FRA/FDJ) 0:00.
36. Thibaut Pinot (FRA/FDJ) 0:00.
37. Adam Hansen (AUS/LTB) 0:00.
38. Arnold Jeannesson (FRA/FDJ) 0:00.
39. Ruben Perez Moreno (ESP/EUS) 0:00.
40. Maciej Bodnar (POL/CAN) 0:00.
41. Niki Terpstra (NED/OPQ) 0:00.
42. Daniele Bennati (ITA/SAX) 0:00.
43. Sylvain Chavanel (FRA/OPQ) 0:00.
44. Aliaksandr Kuschynski (BLR/KAT) 0:00.
45. Jakob Diemer Fuglsang (DEN/AST) 0:00.
46. Matteo Tosatto (ITA/SAX) 0:00.
47. Michael Rogers (AUS/SAX) 0:00.
48. Enrico Gasparotto (ITA/AST) 0:00.
49. Davide Malacarne (ITA/EUC) 0:00.
50. Johnny Hoogerland (NED/VAC) 0:00.
51. Jean-Marc Marino (FRA/SOJ) 0:00.
52. Joaquin Rodriguez (ESP/KAT) 0:00.
53. Steve Morabito (SUI/BMC) 0:00.
54. Pavel Brutt (RUS/KAT) 0:00.
55. Alberto Losada (ESP/KAT) 0:00.
56. Peter Velits (SVK/OPQ) 0:00.
57. Maarten Wijnants (BEL/BKN) 0:00.
58. Bram Tankink (NED/BKN) 0:00.
59. Romain Bardet (FRA/ALM) 0:00.
60. Audrey Amador (CRC/MOV) 0:00.
61. Rui Costa (POR/MOV) 0:00.
62. Kristjan Koren (SLO/CAN) 0:00.
63. Wout Poels (NED/VAC) 0:00.
64. Brian Vandborg (DEN/CAN) 0:00.
65. Laurens ten Dam (NED/BKN) 0:00.
66. Przemyslaw Niemiec (POL/LAM) 0:00.
67. Bauke Mollema (NED/BKN) 0:00.
68. Philippe Gilbert (BEL/BMC) 0:00.
69. Sbastien Minard (FRA/ALM) 0:00.
70. Daniel Moreno (ESP/KAT) 0:00.
71. Jean Christophe Peraud (FRA/ALM) 0:00.
72. Guillaume Levarlet (FRA/COF) 0:00.
73. Maxime Monfort (BEL/RSH) 0:00.
74. Daniel Martin (IRL/GRM) 0:00.
75. Mikel Nieve (ESP/EUS) 0:00.
76. Luis ngel Mat (ESP/COF) 0:00.
77. Mikel Astarloza (ESP/EUS) 0:00.
78. Igor Anton (ESP/EUS) 0:00.
79. Matthew Goss (AUS/ORI) 0:00.
80. Alan Marangoni (ITA/CAN) 0:00.
81. Imanol Erviti (ESP/MOV) 0:00.
82. Simon Gerrans (AUS/ORI) 0:00.
83. Damiano Cunego (ITA/LAM) 0:00.
84. Jos Serpa Perez (COL/LAM) 0:00.
85. Rudy Molard (FRA/COF) 0:00.
86. Daniel Navarro (ESP/COF) 0:00.
87. Haimar Zubeldia (ESP/RSH) 0:00.
88. Manuel Quinziato (ITA/BMC) 0:00.
89. John Gadret (FRA/ALM) 0:00.
90. Marcus Burghardt (GER/BMC) 0:00.
91. Cyril Gautier (FRA/EUC) 0:00.
92. Tejay Van Garderen (USA/BMC) 0:00.
93. Pierre Rolland (FRA/EUC) 0:00.
94. Lieuwe Westra (NED/VAC) 0:00.
95. Tom Veelers (NED/ARG) 0:00.
96. Albert Timmer (NED/ARG) 0:00.
97. Alexis Vuillermoz (FRA/SOJ) 0:00.
98. Amal Moinard (FRA/BMC) 0:00.
99. Anthony Delaplace (FRA/SOJ) 0:00.
100. Kanstantsin Siutsou (BLR/SKY) 0:00.
101. Maxime Mederel (FRA/SOJ) 0:00.
102. Rein Taaramae (EST/COF) 0:00.
103. Hubert Dupont (FRA/ALM) 0:00.
104. Christophe Le Mevel (FRA/COF) 0:00.
105. Rubn Plaza (ESP/MOV) 0:00.
106. Juan Jose Oroz (ESP/EUS) 0:00.
107. Pierrick Fedrigo (FRA/FDJ) 0:00.
108. Laurent Didier (LUX/RSH) 0:00.
109. Andy Schleck (LUX/RSH) 0:00.
110. Markel Irizar (ESP/RSH) 0:00.
111. Jan Bakelants (BEL/RSH) 0:00.
112. Tony Gallopin (FRA/RSH) 0:00.
113. Jens Voigt (GER/RSH) 0:00.
114. Richie Porte (AUS/SKY) 0:00.
115. Assan Bazayev (KAZ/AST) 0:00.
116. Yury Trofimov (RUS/KAT) 0:00.
117. Eduard Vorganov (RUS/KAT) 0:00.
118. Alexey Lutsenko (KAZ/AST) 0:00.
119. Andreas Kloden (GER/RSH) 0:00.
120. Robert Gesink (NED/BKN) 0:00.
121. Stuart O'Grady (AUS/ORI) 2:31.
122. David Millar (GBR/GRM) 0:00.
123. Bart De Clercq (BEL/LTB) 0:00.
124. Julien El Fars (FRA/SOJ) 0:00.
125. Murilo Fischer (BRA/FDJ) 0:00.
126. Jon Izagirre (ESP/EUS) 0:00.
127. Gorka Izagirre (ESP/EUS) 0:00.
128. Jrome Coppel (FRA/COF) 0:00.
129. Cameron Meyer (AUS/ORI) 2:31.
130. Jonathan Castroviejo (ESP/MOV) 0:00.
131. David Veilleux (CAN/EUC) 3:00.
132. Jeremy Roy (FRA/FDJ) 3:00.
133. Simon Clarke (AUS/ORI) 3:00.
134. Lars Ytting Bak (DEN/LTB) 3:00.
135. Simon Geschke (GER/ARG) 3:00.
136. Gatis Smukulis (LAT/KAT) 3:00.
137. Johannes Frhlinger (GER/ARG) 3:00.
138. Ramunas Navardauskas (LTU/GRM) 0:00.
139. Brent Bookwalter (USA/BMC) 3:00.
140. Dmitry Muravyev (KAZ/AST) 3:00.
141. Michael Albasini (SUI/ORI) 3:00.
142. Tom Leezer (NED/BKN) 3:00.
143. Kris Boeckmans (BEL/VAC) 0:00.
144. Thomas De Gendt (BEL/VAC) 3:28.
145. Sep Vanmarcke (BEL/BKN) 0:00.
146. Jrme Pineau (FRA/OPQ) 3:44.
147. Blel Kadri (FRA/ALM) 3:44.
148. Jrme Cousin (FRA/EUC) 3:44.
149. Thomas Voeckler (FRA/EUC) 3:44.
150. Kvin Reza (FRA/EUC) 0:00.
151. Jonathan Hivert (FRA/SOJ) 3:44.
152. Christophe Riblon (FRA/ALM) 3:44.
153. Frederik Willems (BEL/LTB) 3:44.
154. Tom Danielson (USA/GRM) 3:44.
155. Ryder Hesjedal (CAN/GRM) 3:44.
156. Brett Lancaster (AUS/ORI) 3:44.
157. Edvald Boasson Hagen (NOR/SKY) 0:00.
158. Lars Petter Nordhaug (NOR/BKN) 4:01.
159. Peter Kennaugh (GBR/SKY) 4:01.
160. Geraint Thomas (GBR/SKY) 0:00.
161. David Lopez (ESP/SKY) 4:01.
162. Manuele Mori (ITA/LAM) 4:01.
163. Francesco Gavazzi (ITA/AST) 4:01.
164. Jesus Hernandez (ESP/SAX) 4:01.
165. Sergio Paulinho (POR/SAX) 4:01.
166. Juan Antonio Flecha (ESP/VAC) 4:01.
167. Boy Van Poppel (NED/VAC) 0:00.
168. Danny van Poppel (NED/VAC) 0:00.
169. Davide Cimolai (ITA/LAM) 0:00.
170. Romain Sicard (FRA/EUS) 4:01.
171. Moreno Moser (ITA/CAN) 4:01.
172. Alessandro De Marchi (ITA/CAN) 4:01.
173. Svein Tuft (CAN/ORI) 4:01.
174. Lars Boom (NED/BKN) 4:07.
175. Jrgen Roelandts (BEL/LTB) 0:00.
176. Cyril Lemoine (FRA/SOJ) 0:00.
177. William Bonnet (FRA/FDJ) 0:00.
178. Greg Henderson (NZL/LTB) 0:00.
179. Jack Bauer (NZL/GRM) 0:00.
180. Marcel Sieberg (GER/LTB) 0:00.
181. Yukiya Arashiro (JPN/EUC) 0:00.
182. Brice Feillu (FRA/SOJ) 7:09.
