Belgian Thomas De Gendt won the 200-km hilly stage from Macon from a breakaway, ahead of Pinot, the only rider able to follow Alaphilippe’s brutal attack on the last climb with about 13 kilometres left.
The French duo went at full tilt on the descent into St Etienne and held off a trimmed-down peloton at the finish, cheered on by huge crowds hoping to celebrate the first French winner of the Tour since 1985.
The pair crossed the line six seconds behind De Gendt but 20 seconds ahead of the bunch featuring defending champion Geraint Thomas, who suffered a scare 15 kilometres from the finish when he took a minor tumble.
It was breakaway specialist De Gendt’s second stage victory on the Tour after the Lotto Soudal rider prevailed at the top of the iconic Mont Ventoux in 2016.
Alaphilippe now leads Italian Giulio Ciccone, who started the day in yellow with a six-second advantage, by 23 seconds and Pinot by 53 seconds.
Deceuninck Quick Step’s Alaphilippe gained a total of nine bonus seconds and Pinot (Groupama-FDJ) picked up eight at the top of the final ascent and on the finish line.
Thomas is fifth, 1:12 off the pace with his Ineos team mate Egan Bernal a further four seconds adrift.
Vincenzo Nibali, the 2014 champion, dropped out of contention when he cracked on the Cote de la Jaillere and reached the line 4:25 off the pace.
Thomas was frustrated that Alaphilippe’s move came shortly after he had made his way back into the peloton.
“I’m fine but it was just frustrating,” he said. “It was a key moment in the race. (Michael) Woods crashed and took out Gianni (Moscon) and me and I just got tangled in Gianni’s bike.”
Moscon’s bike was snapped in half in the crash.
“By the time I got up to the group I was gassed for a bit and obviously that’s when they started to sprint away,” said Thomas. “It’s annoying and frustrating but to come back like I did is good.
“If I hadn’t crashed I could have followed (Pinot and Alaphilippe) and it’s a totally different story then. Still a lot of racing to go though.”
Sunday’s hilly ninth stage is a potentially treacherous ride from St Etienne to Brioude over 170.5 kilometres.