It was also a career fourth individual stage win on the Tour for the veteran Scottish rider, nine years after his previous win on the world’s biggest bike race.
Millar used all his experience to outfox his rivals in a five-man breakaway as fellow Briton Bradley Wiggins (Team Sky) retained his leader’s yellow jersey.
Following stage wins for Team Sky’s British trio Mark Cavendish, Chris Froome and Wiggins, another member of Team GB’s Olympic selection got in on the act as Millar prevailed on the Tour’s longest stage, a 226km trek through the Rhone valley that featured three categorised climbs.
Millar’s victory was also a boon for his Garmin-Sharp team, whose race was turned on its head in the crashes that marred the opening week of the Tour which saw the withdrawal of their two GC hopes, Ryder Hesjedal and Tom Danielson.
“Two of my previous Tour wins have been in time trials but I won a road stage back in 2002 which was probably my proudest moment on the Tour so it was good to match that,” said Millar.
“Our team was going through turmoil so it was important to get a win. Joining the other Brits with a win bodes well for the Olympics too,” the 35-year-old added.
Two first-category climbs in the opening third of the stage saw numerous groups of riders battle to get away – and even saw a cheeky attack from yellow jersey Wiggins, who pulled clear of the main pack towards the summit of the Col du Granier, 145km from the finish.
An initial group of around 20 riders broke clear shortly after the start in St-Jean-de-Maurienne including the five men who went on to form the day’s main break - Cyril Gautier (Europcar), Egoi Martinez (Euskaltel) and Robert Kiserlovski (Astana), as well as Millar and Frenchman Peraud of AG2R-La Mondiale.
Astana’s Kiserlovski crossed the summit of both climbs in pole position to consolidate the lead of his team-mate Frederik Kessiakoff in the polka dot mountains jersey standings.
The break held a slender lead of just 50 seconds approaching the summit of the Col du Granier thanks to some typically strong pace-setting by Norwegian national champion Edvald Boasson Hagen of Team Sky.
Wiggins then upped the tempo as if to remind the peloton – and perhaps his right-hand man Froome – who was the race’s number one rider. But the Briton was pegged back going over the summit, before a huge downhill attack by Slovak youngster Peter Sagan of Liquigas.
The green jersey managed to join a cluster of riders in pursuit of the five leaders but despite opening up almost two minutes on the peloton, the Sagan group was swept up by the peloton after some hefty work by the Orica-GreenEdge team of Sagan’s green jersey rival Matt Goss.
That left the five-man Millar group with carte blanche to extend their lead over the long and flat middle section of the stage. With Spaniard Martinez the best-placed rider of the five in the GC, more than 25 minutes down on Wiggins, the quintet easily opened up a maximum lead of twelve-and-a-half minutes through the sunny Rhone valley.
Goss won the battle for sixth place in the intermediate sprint to reduce the deficit in the green jersey standings to Sagan, who finished ninth behind the Australian, German double stage winner Andre Greipel (Lotto Belisol) and Dutchman Kenny van Hummel (Vacansoleil-DCM).
The five escapees maintained their large lead as they crossed the summit of the final test of the day, the Cat.3 Cote d’Ardoix 20km from the finish, where Kiserlovski once again took maximum points.
With the peloton still rolling on around 10 minutes in arrears, the battle for the stage win was an odd spectacle as the five leaders almost came to a track-style standstill inside the closing 5km. Two attacks by Martinez and one by Kiserlovski were foiled before Peraud put in a large dig with 2.5km remaining.
Only Millar could follow and the pair rode into a commanding position as they passed under the ‘flamme rouge’. Former mountain bike racer and French national road race champion Peraud was in the hunt for his first UCI win at the age of 35, but he did not have the legs in the closing straight when Millar jumped out of the saddle to take a memorable win.
Martinez took third place five seconds back ahead of Gautier and Kiserlovski. When the peloton crossed the line almost eight minutes later, it was the Australian Goss who pipped Sagan for seventh place - but this was later reversed when the race jury decided Goss has strayed from his line. Sagan now leads his rival by a huge 56 points in the green jersey competition after Goss was slapped with a huge 30-point penalty by the commissaires.
Sky pair Wiggins and Froome finished safely in the bunch alongside GC rivals Cadel Evans (BMC) and Vincenzo Nibali (Liquigas) on a day which saw no change at the top.
Wiggins leads Froome by 2:05 with Nibali in third at 2:23 and Evans fourth at 3:19. The Tour continues on Saturday with the 217km stage 13 from St Paul Trois Chateaux to Le Cap d’Adge which should provide an ideal opportunity for the sprinters to contest a bunch sprint.