The Tinkoff-Saxo rider, who now boasts a 31-point advantage over general classification leader Vincenzo Nibali (Astana) in the race for the polka-dot jersey, secured his second triumph in the last four stages with a determined ride.
Giovanni Visconti (Movistar) took second place having been left behind in the final climb, while Nibali was third as the Italian extended his overall lead.
Having taken on the challenge of the Tour's longest stage on Tuesday, the peloton faced the shortest on Wednesday, but four punishing climbs ensured that it was never going to be an easy day in the saddle.
Small groups of riders made breaks throughout the 124.5-kilometre stage from Saint-Gaudens to Saint-Lary Pla d'Adet, only for the mountain passes to prove a huge leveller and erode their gains.
King of the mountains contender Joaquim Rodriguez (Katusha) took top points on two of the category one climbs, while Team Sky's Vasil Kiryienka claimed 10 points on the other.
As the riders began the final ascent of the day, it was Visconti who made the early break, only for Majka to reel him in, while Nibali's sensational ride on the second half of the 10.2km climb saw his lead over Alejandro Valverde (Movistar) widen to five minutes 26 seconds.
There was an eight-man break at the start of the day but, by the time they made their way up Col du Portillon, the first climb, it had grown to a group of 18.
The descent saw the leading group expand even further as they were joined by four more rivals, including Kiryienka, who took to the front past the halfway stage.
He opened up a gap of almost two minutes after a strong push up Col de Peyresourde, but the chasing pack slowly began to reel him in.
Before the summit of Col de Val Louren Azer, Nicolas Roche (Tinkoff-Saxo) overtook the Belarusian, but Visconti and Majka were in close proximity and positioning themselves for the finish.
Visconti went first but Majka had more in the tank and prevailed by 29 seconds, with a superb finish from Nibali taking him closer to the title.