The 22-year-old, born near Belfort, attacked in the last of seven climbs to cross the line on his own after the Tour crossed the mountainous French border into Switzerland.
Pinot, who was not even selected in the initial choice of Tour riders for his FDJ-BigMat team, was in buoyant mood.
"It's a dream. I rode the longest last 10 kilometres of my life," he said. "I insisted I do it, because I knew what I could do. I hope my team director has no regrets now."
FDJ team manager Marc Madiot's original intention was to keep the young rider back for the Vuelta a Espana (Tour of spain) later this year.