Nibali (Astana) crossed the line of the first high altitude finish of the race with a 10 second gap over second placed Rafal Majka of Poland (Tinkoff-Saxo), with the Czech Republic's Leopold Konig (NetApp-Endura) taking third.
Spaniard Alejandro Valverde (Movistar) finished fourth at 50 seconds and is now Nibali's main rival for the overall victory after Richie Porte of Team Sky collapsed in the sweltering heat, the Tasmanian trickling home alongside team-mates Mikel Nieve and Geraint Thomas more then nine minutes down to drop out of the top ten.
Valverde is 3:32 down on Nibali ahead of Saturday's second stage in the Alps, with Frenchman Romain Bardet (Ag2R-La Mondiale) third at 4:24 after finishing seventh at the ski resort Chamrousse.
Winner of the 2011 Vuelta a Espana and 2013 Giro d'Italia, Nibali made his decisive attack on the final of three climbs, 6.5km from the finish of the 197.5km stage from Saint-Etienne. With his nearest rival Porte already struggling with illness, Nibali soon bridged the gap to Majka and Konig before riding clear inside the final 3km.
Valverde had been the first of the GC riders to launch an attack just over 10km from the summit - prompting a delayed reaction from both Nibali and Pinot.
Once Nibali rode clear, Valverde and Pinot remonstrated and argued instead of combining in the chase, both riders perhaps already thinking about securing a place on the podium in Paris rather than targeting a maillot jaune that looks very much glued to the shoulders of the Sicilian, Nibali.
"It's a special day for me today and I'm very happy," said Nibali, winner of stage two at Sheffield and stage 10 at La Planche des Belles Filles.
"I wanted to gain as much time as possible over Porte and Valverde. Porte had a problem and was dropped so it was just Valverde left to drop. I felt stronger than him and so attacked. But it was so hot today - it felt like Palermo in my home island of Sicily."
Nibali, who also moved into the lead of the king of the mountains competition, also payed homage to two-time Tour champion Gino Bartali on the 100th anniversary of the Italian campionissimo's birth date and to the late Fabio Casartelli, who tragically died exactly 19 years ago during the 1995 Tour de France.
NINE-MAN BREAK: Giovanni Visconti (Movistar), Alessandro De Marchi (Cannondale), Blel Kadri (Ag2R-La Mondiale), Kristijan Durasek (Lampre-Merida), Daniel Oss (BMC), Rudy Molard (Cofidis), Jan Bakelants (Omega Pharma-Quick Step), Bartosz Huzarski (NetApp-Endura) and Brice Feillu (Bretagne-Seche) broke clear of the peloton on the Cat.1 Col de la Croix de Montvieux to build up a maximum lead of five minutes as the riders left the Loire and entered the department of Isere.
With temperatures rising to 40 degrees centigrade in the valley, the break struggled to keep their momentum going and their advantage soon came crashing down. Buy the time the escapees reached the foot of the Cat.2 Col de Palaquit, 45km from the finish, their gap had dropped to under two minutes. The climb - making its debut in the Tour de France - dealt a punishing blow to all but De Marchi and Bakelants, the Italian crossing the summit with one minute over the Belgian, as Spain's Luis Mate (Cofidis) crossed ahead of the peloton that trailed De Marchi by 2:45.
The Italian rode through the intermediate sprint back in the valley at Grenoble with an advantage of 3:30 but he - along with both Bakelants and Mate - was reeled in early on the final climb. A nasty crash on the descent of the Palaquit saw Nibali deprived of one of his key mountain lieutenants, Jakob Fuglsang. But such is the imposing form of Nibali in the absence of pre-race favourites Chris Froome and Alberto Contador, the 29-year-old did not need anyone's help to secure a famous Tour hat-trick and extend his lead at the top.
RIDE OF THE DAY: Vincenzo Nibali did not even look out of breath as he crested the summit at Chamrousse to defy the stifling temperatures and put half a foot on the podium in Paris thanks to a third Tour stage win. Messrs Froome and Contador would have perhaps struggled to match the Italian on the race's first day in the Alps.
DAY TO FORGET: Richie Porte battled with illness and finished nine minutes down after imploding spectacularly on the final climb as Team Sky's race took another turn for the worse. Porte dropped out of the top ten and will have done little to defy the critics who claim the Australian does not have what it takes to be an overall threat in Grand Tours. Spare a thought also for Spain's Dani Navarro, who was forced to withdraw from the Tour on his 31st birthday after struggling with sunstroke and illness.
COMING UP: A second day in the Alps sees the riders tackle both the Col du Lautaret and the Col d'Izoard before a final showdown on the slopes to Risoul. The 177km stage 14 from Grenoble is the pick of the two Alpine stages - and temperatures are set to be a little more clement and so we can expect some attacks from riders with a point to prove.
PLAT DU JOUR: There is a cafe in the centre of Briancon - where the riders will take on their own musettes ahead of the Izoard - which serves a 'Serre Che' burger that comes with melted reblochon cheese, bacon and a rare patty inside a soft brioche bun. Divine.
STAGE IN A SENTENCE: The Shark eats up the field before spitting out Porte and stealing Purito's polka dots.
- Sports & Recreation
- Richie Porte
- Alejandro Valverde
- Tour de France
- Alessandro De Marchi
- Leopold Konig