As France experienced a heatwave defending champion Thomas mis-timed a curb and was left with a gash on his left leg after hitting the tarmac hard on the 177km run around the southern city of Nimes.
After his third fall during this Tour, Team Ineos' sports director Nicolas Portal said Thomas felt fine.
"He's OK, he needed another bike. All his left side is a bit messed up but nothing serious," he said.
"We have to refocus after the rest day," added Portal.
Thomas remains 1min 35sec behind Alaphilippe in the overall standings, with the following three riders all within 27 seconds ahead of three challenging days in the Alps.
He also tumbled after flying over a barrier in the wild atmosphere in Brussels on the opening day, and again on the road to Saint-Etienne on stage eight.
This time the 33-year-old had no problem getting back to the pack on a flat stage with no wind to split the peloton.
The popular 2018 Tour de France champion was sweating at the start line alongside the spectacular stone bullring known as the Arena in downtown Nimes.
"I'm just concentrating on keeping fuelled and hydrated and getting to the end of the race," he said before embarking.
Thomas's teammate the 22-year-old Colombian Egan Bernal, who is fifth 27 seconds behind Thomas but 2min 02sec behind Alaphilippe was a picture of serenity after the race.
"Okay it was hot but it wasn't so bad," said Bernal, who has the best under-25's white jersey.
"I rather like these conditions and to be honest I'm looking forward to the Alps. In terms of altitude it'll be like in Colombia" he said.
"The day off really did me good, I feel great today."
Bernal said that Thomas was in good shape despite his heavy fall.
"I spoke to him just now and he's seen the doctor already and he's just got a couple of cuts, nothing serious" said Bernal.
"It was nothing out of this world, there must have been something on the road."
Alaphilippe has been hugely active signing autographs with the French public the past two weeks, but went straight to his team bus Tuesday and did not reappear.
Ewan meanwhile was following up his victory on stage 11 at Toulouse and with Nimes melting under 35 degrees Celsius (95 Fahrenheit) the Australian was favourite for a repeat performance, this time edging Italian Elia Viviani on the line.
"I'll look back on this Tour and say it was a success," said the diminutive Ewan. "This is the furthest I have ever been in a Grand Tour, I've never finished one before."
Peter Sagan, who came fourth on the day but is in the green sprint points jersey, said it was too hot to race and that something should be done to protect riders.
Dehydration was a major issue as team cars were carrying an average of 200 water bottles, many of them with added minerals and saline with riders expected to drink 15 of the half litre bidons each.
Some fans stayed away due the extreme afternoon heat on this southern French route, but the conditions failed to slow the peloton as it sped past the celebrated regional vineyards and olive groves.
One of the pre-race favourites Jakob Fuglsang, the Criterium du Dauphine champion, pulled out with 25km to go after falling and hurting his hand.
Wednesay's 17th stage sees the Tour head north towards its Alpine reckoning with a 200km run from the Pont du Gard bridge in the Camargue to Gap, where bonus seconds atop a climb 10km from the finish line ensure further drama ahead of the three much awaited stages that follow it.
Results from stage 16 of the Tour de France around Nimes on Tuesday:
1. Caleb Ewan (AUS/LOT) 3hrs 57min 08sec.
2. Elia Viviani (ITA/DEC) same time.
3. Dylan Groenewegen (NED/JUM) 0.
4. Peter Sagan (SVK/BOR) 0.
5. Niccolò Bonifazio (ITA/TDE) 0.
6. Michael Matthews (AUS/SUN) 0.
7. Matteo Trentin (ITA/MIT) 0.
8. Jasper Stuyven (BEL/TRE) 0.
9. Alexander Kristoff (NOR/UAE) 0.
10. Andrea Pasqualon (ITA/WGG) 0.
11. Jens Debusschere (BEL/KAT) 0.
12. Edvald Boasson Hagen (NOR/DDT) 0.
13. Sonny Colbrelli (ITA/BAH) 0.
14. Maximiliano Richeze (ARG/DEC) 0.
15. André Greipel (GER/ARK) 0.
16. Reinardt Janse Van Rensburg (RSA/DDT) 0.
17. Oliver Naesen (BEL/ALM) 0.
18. Warren Barguil (FRA/ARK) 0.
19. Greg Van Avermaet (BEL/CCC) 0.
20. Julian Alaphilippe (FRA/DEC) 0.
24. Mikel Landa (ESP/MOV) 0.
25. Geraint Thomas (GBR/INE) 0.
27. Steven Kruijswijk (NED/JUM) 0.
28. Egan Bernal (COL/INE) 0.
29. Thibaut Pinot (FRA/FDJ) 0.
35. Rigoberto Uran (COL/EF1) 0.
36. Simon Clarke (AUS/EF1) 0.
37. Daniel Martin (IRL/UAE) 0.
38. Richie Porte (AUS/TRE) 0.