The 22-year-old Frenchman was urged every inch of the way by Directeur Sportif Marc Madiot after making his decisive break over the final climb of the day - the first category Col de la Croix.
The group of favourites were led over the line by Cadel Evans (BMC), 26 seconds behind Pinot. Wiggins (Sky) retains the yellow jersey having held off an attack on the descent by Vincenzo Nibali (Liquigas) and a late surge by Evans to finish on the same time as his nearest rivals.
However, the day belonged to Pinto and at just 16km from the finish and with a two minute gap over the leaders, he was always favourite to take the win.
Short and painful was the way most people were describing this stage from Belfort to Porrentruy with seven categorised climbs over a distance of 157.5km. And while most had been predicting that a small break away would make it the whole way to the finish, the peloton had other ideas.
Jens Voigt (Radioshack Nissan) was the most determined of the early breakaway riders as he powered over the first two climbs of the day on his own. Behind him a group of riders went from eight to 12 and rose at one stage to 23 although they were never too far from the eyes of the peloton. Voigt eventually ran out of steam and without any assistance fell away with 60km raced.
Samuel Sanchez (Euskaltel Euskadi) joined the list riders forced to abandon after a crash at 57km saw him break his wrist, collar bone and dislocate his shoulder. Along with forcing Sanchez out of the Tour, this crash will also see the Spanish Olympic team further depleted following the loss of Oscar Friere through an earlier Tour crash. Alessandro Valverde (Movistar) was also caught up in this crash but climbed back on his bike and received running repairs from the Tour doctor.
At the halfway point in the stage, Pinot's teammate, Jeremy Roy rode out of the peloton and straight past the breakaway group before being joined by Astana's Fredrik Kessiakoff. The pair rode together until the ascent of the Category 2 Cote de Saulcy at the 97km mark, where Swede Kessiakoff made his attack. This attack saw Kessiakoff build up a lead of 1'40” at one point over the chasing group, which included Pinot.
It wasn't until the penultimate climb of the Category 2 Cote de la Caquerelle at 130km, that Frenchmen Pinot and Radioshack Nissan's Tony Gallopin set off in pursuit of the plucky Swede and seemed to be working well together, however, as they reached the Category 1 Col de la Croix, Gallopin's legs gave way and Pinot set off in chase on his own.
Having been alone over some severely undulating terrain, Kessaikoff had nothing left to give when, nearing the top of the climb, Pinot rode up to and shot past the flagging Swede. The stage was now Pinot's to lose and with Madiot offering him some gentle words of encouragement all the way to the line, he was unlikely to stop driving.
Kessaikoff was swallowed up by the favourites on the run down to the finish, while Tony Gallopin's brave effort didn't go unrewarded as he finished third and moved up in the white jersey classification.