Spain’s Alejandro Valverde (Movistar) had been second overall, but dropped to third, and is now one minute five seconds behind.
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Valverde finished six seconds behind, dropping to third overall and 1:05 behind Quintana.
Chris Froome described winning on the Peña Cabarga for a second time as an incredible feeling.
It was all back together in the front group as they approached Pena Cabarga, however – but the advantage was just 18 seconds ahead of the peloton as the climbing started. Esteban Chaves (Orica-BijeExchange) and Contador complete the top five – although both riders slip further behind despite a spirited attack by the former on Wednesday’s decisive climb.
The Tinkoff rider hinted that his objective might be to get a stage win during the second half of the Vuelta, “I’m going to have a look at the stages and decide what to do.” he said.
Leopold Konig was alongside his Team Sky leader, too, and it was the Czech’s efforts which closed the gap to Chaves as the gradient approached the one-in-five mark again.
Chaves was dropped and Froome sat on Quintana’s wheel before accelerating for a long-awaited stage win.
“I’m three minutes behind Nairo Quintana whose doing really well and who has a good team behind him”.
“I’m just trying to do as much as I can day by day now, and I hope that obviously I can keep getting closer to him”.
A brief ceasefire ensued when the road flattened out on the penultimate hairpin of the climb before Froome put in a trademark surge to sweep past Quintana and take his first win of the race.
Race leader Quintana waited even longer, however, until he reached around 800m from the finish.
“I want as much time, he wants as much time – that’s what makes the race exciting”.
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Thursday’s 12th stage is a mountainous 193.2-kilometer (120-mile) route from Los Corrales de Buelna to Bilbao in the Basque Country.
