Alaphilippe now leads by 23 seconds from Ciccone with Pinot third, 53 seconds down.
Since achieving a third-place finish in 2014, Pinot has always struggled at his home race, and skipped it a year ago.
They could not catch De Gendt, the Belgian who won by six seconds, but beat Ciccone by 20 seconds for Alaphilippe to regain the yellow and wear it on Sunday for the 14 July festivities.
Thomas De Gendt celebrates his incredible stage win.More news: Minecraft Earth Gameplay Looks Adorable
"Jumbo-Visma's George Bennett retains fourth place, 70 seconds off the pace, with Thomas" deficit in fifth now 72 seconds.
"It was a fantastic finale, it was handsome to go together like this and we showed that we can work together even if we're in different teams", said Alaphilippe, whose move was highly expected as bonus seconds were up for grabs in the ascent to the Cote de la Jaillere and at the finish. I got tangled in Gianni's bike and took some time to get going. "It's annoying and frustrating but to come back like I did is good". If I hadn't have crashed I could have followed, and it's a totally different story today.
Echoing former teammate Porte, Thomas highlighted the threat that the French pair pose heading into the second week.
French duo Thibaut Pinot, right, and Julian Alaphilippe cross the finish line after a fine day for the locals.
Thomas was involved in another crash during the opening stage last week in Belgium.More news: NY power outage knocks out subways, businesses, elevators
"I've been working hard for that, but it goes beyond my hopes", Alaphilippe said. Woods later rode in with torn shorts. "It's just unfortunate I can't get into free wind in the bunch sprints", Matthews said. De Gendt sniffed a chance on the Cote de la Jailliere and took it.
De Gendt rode away immediately after the 200km stage from Macon kicked off alongside three other riders, and was the last survivor of the leading quartet not to be caught by the peleton.
"The [general classification] teams took over midway through the day and tried to help and bring the break back ... we started pulling straight away to bring back the three guys ahead but unfortunately we fell just short".
A day after his long and unsuccessful breakaway in Burgundy, Frenchman Yoann Offredo struggled with an intestinal bug at the back while pure sprinters including Dylan Groenewegen and Caleb Ewan went through a day of suffering, just making sure they reached the finish within the delays.More news: Huawei to raise Dollars 1.5 bln to finance in-house development