The day's laurels went to Spaniard Ruben Plaza Molina although the action was way behind as Froome's key lieutenant Thomas was sent flying off the road.
In a tricky final descent Thomas bumped into Frenchman Warren Barguil and collided head first into a telegraph pole, disappearing over the road into the vegetation.
"Everyone was anticipating that descent as a critical moment of the race," Froome said.
"I think there is some riders who look to gain some time in moments like that I think we've seen Nibali riding in similar fashion and we can expect more of that in the next few days."
Thomas said: "I was just taken out."
The Welshman, who is sixth overall, was quickly back on his bike and reached the finish incurring only minor losses.
"I apologise I wanted to brake just before the bend but (American) Tejay van Garderen pushed me with his shoulder and my finger slipped from the brake lever, I'm sorry," said Barguil.
Froome, who also lost team mate Peter Kennaugh as the British champion abandoned the race, said: "He's OK he's a tough guy he's going to be up there in the Alps."
The incident brought back memories of the 2003 Tour, when Spain's Joseba Beloki, who was trailing Lance Armstrong in the overall standings, attacked on the same descent and crashed out of the race.
Armstrong avoided Beloki and in the process cycled down the hill across a small field and, after jumping over a ditch, rejoined the road.
Among his main rivals, only Alberto Contador attacked Froome in the climb up the Col de Mense but the Spaniard could not open up a telling gap.
Defending champion Vincenzo Nibali, who fell out of contention in the Pyrenees, also attacked to pull away but Froome did not bother chasing the Italian on another hot day on the Tour.
Plaza Molina of the Lampre team won solo after a 201-km ride from Bourg de Peage, attacking a group of breakaway riders in the final climb of the day.
Slovakian Peter Sagan of Tinkoff-Saxo was second for the fifth time on the Tour this year despite riding spectacularly in the descent, while Colombian Jarlinson Pantano took third place for IAM Cycling.
Froome still leads Colombian Nairo Quintana by three minutes and 10 seconds and third-placed Van Garderen is 3:32 off the pace going into Tuesday's rest day.
The race will then enter a crucial spell with four gruelling stages in the Alps.
(This story corrects second and third placings in overall standings in penultimate para)
(Reporting by Julien Pretot; Editing by Tom Hayward)
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