"They've got some real punch," Thomas said. "They're the ones to watch."
Alaphilippe abandoned his yellow jersey for just 6s to Giulio Ciccone at the Planche des Belles Filles ski station. He knew he had a golden chance to get it back on rollercoaster terrain suiting his skills.
"I will wear the yellow jersey on Bastille Day — for a Frenchman, there is nothing better," Alaphilippe said after finishing the stage third, just behind Pinot.
Thomas De Gendt won the 200km trek after a long breakaway effort at the front.
With bonus seconds at play at the summit of the final categorised climb, the Cote de la Jaillere, Alaphilippe surged from a small pack of favourites near the top, with Pinot on his wheel.
The brutal attack was left unanswered and Alaphilippe went over the mountain in second position behind De Gendt, claiming five precious bonus seconds. Working well with Pinot, they went all out in the downhill and kept the pressure on in the final kilometres.
Alaphilippe turned his deficit to Ciccone into a 23s lead over the Italian, with Pinot third, 53s off the pace.
Since achieving a third-place finish in 2014, Pinot has always struggled at his home race and skipped it last year.
Fifth overall and 1m 12s behind Alaphilippe, Thomas crashed about 15km from the end but escaped unscathed and crossed the finish line 20s behind Alaphilippe and Pinot. The pile-up involved other Ineos riders and left one of his teammates' bikes broken in two pieces.
Once back in the pack, the Welshman did not move when Alaphilippe and Pinot went away.
Thomas was involved in another crash during the opening stage last week in Belgium.
This time, he said he was taken out by Michael Woods when the Canadian rider crashed going around a right-hand bend. Woods later rode in with torn shorts.
Thomas took consolation from the fact he was able to catch up with the speeding pack but was disappointed Pinot and Alaphilippe got away.
"The good thing is I had good legs to be able to [catch up]. It's just frustrating that those two got time."
- AP