Benat Intxausti of Spain, riding for the Movistar team, won the stage, a 238km ride from the French resort of Valloire, in 5hr 52.48min.
Intxausti beat Estonian Tanel Kangert into second in a sprint finish, with Nibali and his rivals in the general classification, Australian Cadel Evans and Colombian Rigoberto Uran, coming in as part of the same peloton 14sec behind.
Evans stands 1min 26sec off Nibali, with Uran 2.46 off the Italian's pace.
Stage results (country/team):
1. Benat Intxausti (Spain / Movistar) 5:52:48"
2. Tanel Kangert (Estonia / Astana) ST
3. Przemyslaw Niemiec (Poland / Lampre)
4. Ramunas Navardauskas (Lithuania / Garmin) +14"
5. Cadel Evans (Australia / BMC Racing)
6. Franco Pellizotti (Italy / Androni Giocattoli)
7. Michele Scarponi (Italy / Lampre)
8. Rafal Majka (Poland / Saxo - Tinkoff)
9. Jose Herrada (Spain / Movistar)
10. Carlos Betancur (Colombia / AG2R)
Overall standings:
1. Vincenzo Nibali (Italy / Astana) 67:55:36"
2. Cadel Evans (Australia / BMC Racing) +1:26"
3. Rigoberto Uran (Colombia / Team Sky) +2:46"
4. Michele Scarponi (Italy / Lampre) +3:53"
5. Przemyslaw Niemiec (Poland / Lampre) +4:13"
6. Mauro Santambrogio (Italy / Vini Fantini) +4:57"
7. Carlos Betancur (Colombia / AG2R) +5:15"
8. Rafal Majka (Poland / Saxo - Tinkoff) +5:20"
9. Benat Intxausti (Spain / Movistar) +5:47"
10. Domenico Pozzovivo (Italy / AG2R) +7:34"