Pinot of the FDJ-BigMat team steadily moved up from the back of the field and grabbed the lead 550 yards before the top of the final of seven climbs along the 97-mile trek from Belfort to Porrentruy in Switzerland.
He held off Jurgen van den Broeck and defending champion Cadel Evans for the stage victory, clocking in with a time of 3 hours, 56 minutes and 10 seconds.
Australia's Evans claimed second place, just ahead of Britain's Wiggins, 26 seconds behind Pinot.
Wiggins hung onto a 10-second lead over Evans in the race for the overall championship.
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