He finished 1.16 seconds ahead of Germany's Stefan Luitz, with Park City's Ted Ligety climbing up from sixth to finish 1.42 behind in third place on the Stade Olympique de Bellevarde course.
Pinturault was left just as stunned as the home fans by his error as he caught an inside ski and put his hand down with the finish line in sight, missing out on the chance of a second straight success after winning Saturday's slalom.
Ligety, meanwhile, has got his third podium of the season but missed out on a hat trick of giant slalom victories after winning the last two races.
"Val d'Isere's always tough, it's not a hill I particularly like," Ligety said. "It's not very user friendly, it's very steep the whole way."
Ligety was unhappy with his first run, where he finished sixth, but found some satisfaction with his second.
"I'm happy to salvage it," he said. "I'm happy to walk away from this hill with a podium when it could easily have been a DNF."
In St. Moritz, Switzerland, Tina Maze of Slovenia won her third straight World Cup giant slalom to extend her lead in the overall standings, and defending champion Lindsey Vonn placed 27th after almost crashing out.
Maze held her morning lead to finish 0.08 seconds ahead of Viktoria Rebensburg, the Olympic champion from Germany, in a total time of 2 minutes, 11.07 seconds. Tessa Worley of France was third, trailing Maze by 0.55.
Vonn hit trouble midway down her second run after her skis appeared to touch. The American racer came out of rough, course-side snow to complete the race nearly six seconds slower than Maze and score four valuable World Cup points.
In Winterberg, Germany, World Cup titleholder Alexander Zubkov won his fourth consecutive four-man bobsled race to extend his lead in the season standings.
Pushed by Alexey Negodaylo, Dmitry Trunenkov and Maxim Mokrousov, Zubkov beat World Championship runner-up Maximilian Arndt of Germany and his crew of Alex Mann, Alexander Roediger and Martin Putze by 0.19 seconds.
After four of nine races, Zubkov leads with 900 points. World and Olympic champion Steven Holcomb of Park City, who finished sixth, is second with 788 points. Arndt is third with 722.