Pantano outsprinted breakaway companion Rafal Majka (Tinkoff) of Poland at the end of a 160-km trek in the Jura mountains to give his IAM Cycling team, who will be folding at the end of the season, a first victory on the Tour.
"I dreamt of this all my life, I'm so happy," Pantano said.
"Majka had won several Tour stages (three) and I was wary of him in the finale but I had good sensations. I knew that if I was catching him in the descent I'd have a good chance to win."
Briton Froome retained the overall lead after his Team Sky easily controlled feeble attacks from top-10 riders Fabio Aru, Alejandro Valverde and Romain Bardet.
Frenchman Bardet's attack, however, hurt American Tejay van Garderen, who lost 1:28 to the leading riders and slipped from sixth to eighth overall as his hopes of a podium finish in Paris took a serious knock.
Froome leads Dutchman Bauke Mollema (Trek-Segafredo) by 1:47 and third-placed Briton Adam Yates (Orica-Bike Exchange) by 2:45.
A 30-man group broke away on the first of the six ascents of the day, up to the Col du Berthiand.
It featured seven Tour stage winners including 2014 champion Vincenzo Nibali, Frenchmen Alexis Vuillermoz, Pierre Rolland and Thomas Voeckler, Dutchman Tom Dumoulin, Majka as well as Spain's Ruben Plaza.
Punishing climb
Swiss Sebastien Reichenbach, who started the Tour as Frenchman Thibaut Pinot's lieutenant, was the best-placed rider in the overall standings as he started in 17th place, 11:41 off the pace.
After several foiled attacks, a group of 13 were in front, including Reichenbach while Nibali and Dumoulin were dropped in the ascent to the Col du Grand Colombier, a punishing 12.8-km climb at an average gradient of 6.8 percent.
Russian Ilnur Zazkarin and Majka jumped away from the group 5km from the top and the Pole went solo in the final ascent on the Lacets du Grand Colombier, an 8.4km climb at 7.6 percent.
Pantano, however, descended at breakneck speed to rejoin Majka and he was far too strong in the final sprint.
At the front of the main pack, Astana's brutal acceleration set up an attack by 2015 Vuelta champion Aru in the last climb.
The Italian was followed by Spain's Valverde, only for the duo to be quickly reined in by Froome's team mates Mikel Nieve and Wouter Poels.
Bardet (AG2r-La Mondiale) then attacked near the summit and while the move did not threaten Froome, it was fatal for Van Garderen, who is now 4:47 off the overall pace.
Monday's 16th stage is a 209-km ride from Moirans-en-Montagne to Bern. The peloton will then enjoy a rest day before the final week in the Alps.
