The 21-year-old had claimed his first World Cup win in a city event in Moscow last winter but it could not compare with beating the world's best at home on the steep Face de Bellevarde slope used for the 1992 Olympics.
In a combined time of one minute and 36.55 seconds, Pinturault left Germany's Felix Neureuther 0.50 seconds adrift with Austria's overall World Cup champion Marcel Hirscher was third, a further 0.07 behind.
Pinturault is one of the most promising talents produced by French skiing in recent years, having earned podium places in four alpine disciplines since his World cup start two seasons ago.
He made it clear that his long-term ambition was to win the overall World Cup big globe.
"I'm not going to lie about it. The World Cup is my ambition and I want to get there. But I'm taking my time, and going each step at a time," he said.
His show of strength was all the more impressive as the Frenchman injured his ankle playing tennis in the summer and could not train for three months.
"This does not have the same flavour as Moscow. The conditions were difficult for me because of my ankle. I was short on training and I managed to win at home in France.
"It's a special one, obviously," said Pinturault.
The conditions were also special as the second leg was floodlit, organisers having been forced to postpone the race because of heavy snowfalls overnight.
Hirscher collected his fourth podium place in succession in technical events and made it back to third in the overall World Cup standings, 120 points behind Norway's Aksel Lund Svindal.
Asked about Pinturault, the Austrian said: "I'm not surprised by his victory. I've known him since the junior ranks and I know what he's worth. It was bound to happen and it's good for skiing to have such young talent," he said.
However, he should not worry too much about the Frenchman stealing the limelight right now as Pinturault said he would be cautious for the rest of the season to help his ankle heal.
"I'm going to pick my races and do fewer speed events because I didn't have much training in downhill," he added.
Pinturault's victory was the fourth in Val d'Isere by a Frenchman in the World Cup and he will be among the favourites again in Sunday's giant slalom with Hirscher and American Ted Ligety.
- Sports & Recreation
- Marcel Hirscher