The Australian veteran outfoxed four fellow escapees in the longest stage of the race as Frenchman Thibaut Pinot leapfrogged compatriot Romain Bardet into the top three in the overall standings.
Tinkoff-Saxo's Rogers proved the strongest on the descent off the back of the Port de Bales climb to cross the finish line nine seconds ahead of Thomas Voeckler (Europcar), Vasil Kiryienka (Team Sky), Jose Serpa (Lampre-Merida) and Cyril Gautier (Europcar).
A pulsating first day in the Pyrenees saw Italy's Vincenzo Nibali (Astana) preserve his lead over second-place Alejandro Valverde (Movistar) but all change behind as the likes of Ag2R-La Mondiale's Bardet, American Tejay van Garderen (BMC) and Dutchman Bauke Mollema (Belkin) all cracked on the deciding climb to lose time at the finish.
FDJ's Pinot put in a series of stinging attacks on the fifth climb of the 237.5km stage to force a selection in the main group of favourites, which had trailed the Rogers escape group by over 10 minutes at the foot of the final ascent.
First Van Garderen, then Mollema and then Bardet were blown off the back - the power of Pinot matched only by the yellow jersey Nibali, Spaniard Valverde and his Movistar team-mate John Gadret, and French veteran Jean-Christophe Peraud, who clearly chose not to sit up and wait for his Ag2R team-mate Bardet.
Bardet, wearing matching white shorts with his white jersey as the race's best young rider, cut a lonely figure on the steep incline of the Port de Bales, his plight made all the worse when Pinot's FDJ team-mate Arnold Jeannesson joined the Nibali group to help drive the pace for Pinot.
Meanwhile, on the front of the race, Serpa crossed the final summit ahead of Voeckler and Rogers ahead of the 21km descent towards the finish, with Kiryienka and Gautier cresting just 20 seconds in arrears.
The five riders came together on the descent with Europcar holding the numerical advantage: already, Rogers had had a word with Voeckler - twice a Tour stage winner in Luchon - after he took exemption to the French veteran's bid to slow the pace and wait for his team-mate Gautier.
"I told him, 'no, listen, you're not going to beat me like that today'. I've been in this position too many times before not to win," Rogers later told reporters after picking up a first career stage win on the Tour. "I knew once it got towards the bottom of the last ascent that the race would begin for me. Voeckler has a team-mate behind so I used it as a bargaining chip."
Gautier had surged clear with around 5km from the finish but Rogers counter-attacked and opened up a big enough gap for him to put his head down and time trial towards the finish.
It was the 34-year-old's third big win of an initially troubled season, the Australian veteran having notched two wins on the Giro d'Italia after being cleared for testing positive for the anabolic steroid clenbuterol during the Japan Cup last October.
"I've tried so hard in the past to win a stage on the Tour. It's amazing," an emotional Rogers said. "I'm more hungry now than before - the opportunities seem clearer to me now. Previously I was scared to try something because I was afraid of failure."
As Rogers bowed to the people of Luchon while crossing the line, the fierce battle for the general classification continued behind. Pinot was joined by another FDJ team-mate, Jeremy Roy, who had been part of the initial break, and although the notoriously meek descender lost touch with Nibali and Valverde on one occasion during the long descent, he managed to fight back on to finish alongside his rivals 8:32 down on Rogers.
Pinot rose to third on GC after Bardet came home almost two minutes further back, with Van Garderen dropping to sixth place after losing almost four minutes following a troubled final ascent.
Nibali goes into Wednesday's brutal stage to Saint-Lary Pla d'Adet with a lead of 4:37 on Valverde and 5:06 on Pinot. Peraud is fourth on GC at 5:08 and above team-mate Bardet who now trails Pinot, the new white jersey, by 1:34 and Nibali by 6:40.
TWENTY-ONE-MAN GROUP: Numerous moves and counter moves took place in the first hour or so before the race settled and a large group of 21 riders formed after the first two minor climbs, the Cat.4 ascents at Fanjeaux and Pamiers.
The experienced group included eight former Grand Tour stage winners in Rogers, Kiryienka, Voeckler, Jon Izagirre (Movistar), Michael Albasini (Orica-GreenEdge), Jan Bakelants (Omega Pharma-Quick Step), Tony Gallopin (Lotto-Belisol) and Samuel Dumoulin (Ag2R-La Mondiale), as well as the likes of Sky's Bernhard Eisel, BMC's Greg van Avermaet, Europcar pair Gautier and Kevin Reza, Omega Pharma-Quick Step's Michal Kwiatkowski and the moustachioed Colombian Serpa.
With Polish youngster Kwiatkowski - the highest placed rider on GC - the best part of 20 minutes down on GC, the Astana team of Nibali were happy to let the break build up a maximum lead of 12:45 under the blue skies and bright sun of the Pyrenean foothills to the west of Carcassonne.
Voeckler took maximum points over the Col de Portet d'Aspet and the Col des Ares before the jostling began on the decisive climb. Early attempts by both Voeckler and Roy were neutralised before Kiryienka set a fast tempo that saw the leading group whittled down to single figures.
Gautier attacked near the summit and was followed only by Voeckler, Rogers and Serpa. When Gautier tired and dropped back, he was joined by Kiryienka and the pair rode in pursuit of the leading trio, who crossed the summit with a 20-second advantage before the long descent to Luchon.
Meanwhile, back with the peloton Movistar dictated play - with Gadret and Benat Intxausti driving a fierce pace to shed the main pack and put the likes of Bardet, Van Garderen and Mollema on the ropes. When Pinot decided to come to the front with Jeannesson, it proved too much for the stragglers and they sunk like stones.
Such was Pinot's impressive climbing that he opened up a small gap over both Nibali and Valverde as he crested the summit in control.
"I was feeling good and managed to take some time back," Pinot said after the stage. "Tomorrow is probably the hardest stage of the Tour. I will try and follow Nibali and Valverde and then drop them on the final climb."
RIDE OF THE DAY: Mick Rogers' win was almost a carbon copy of his stage 11 win in the Giro, where he attacked on the final climb and distanced the chasing pack on the descent to Savona - where he won by 10 seconds. This time round his lead was one second less, but his victory all the more impressive. With Voeckler and Gautier, Europcar had the numerical advantage - and Rogers needed to use all his experience to emerge victorious.
Rogers' performance aside, praise must go to Thibaut Pinot - who was explosive - and the tactics of his FDJ team, with the likes of Jeannesson and Roy both playing a big role in seeing their man take the white jersey and rise onto the podium.
DAY TO FORGET: Both Romain Bardet and Tejay Van Garderen were found wanting in this first of three showdowns in the Pyrenees. The American will at least have the time trial to use as a tool of clawing back lost time - but Bardet will need to attack in stages 17 and 18 if he wants to keep his dreams of a podium finish alive.
COMING UP: Wednesday's short but sharp 124.5km stage 17 from Saint-Gaudens to Saint Lary features four killer climbs, including the fearsome Col du Peyresourde, ahead of the HC finish at Pla d'Adet. The time gaps could be phenomenal.
STAGE IN A SENTENCE: Pinot gloire as Bardet and Van Garderen struggle on a day Rogers denies Voeckler a Luchon treble.
- Sports & Recreation
- Thomas Voeckler
- Romain Bardet
- Thibaut Pinot
- Vincenzo Nibali
- Cyril Gautier
- Vasil Kiryienka
- Tejay van Garderen