The shortest normal stage of the race for 30 years was expected to cause ripples in the general classification, with the 65 kilometre route featuring a tough climb up the Col de Portet.

Shortly after the first-ever Formula One style grid start, introduced by organisers and arranged by general classification ranking, riders ascended the Col de Peyresourde.

A breakaway group were allowed to move clear, the move slowly reducing in size as three quick climbs took their toll.

Estonia’s Tanel Kangert was left solo in the lead, but his advantage faded as attacks began in the peloton.

Ireland’s Dan Martin and Quintana moved clear of the general classification group as the Col de Portet began.

Quintana put distance between himself and Martin as the Movistar rider began moving past the remnants of the breakaway.

The Colombian soon caught Kangert and, after a brief spell leading with Poland’s Rafal Majka, went clear with six kilometres of racing to go.

Quintana finished alone to clinch a first stage win at the race since 2013, crossing the line in 2 hours 21min 27sec.

Martin finished second 28 seconds down to end as the runner-up on the stage.

A late acceleration from Thomas saw the Welshman clinch additional seconds over his general classification rivals, the Team Sky rider finishing 47 seconds down on the winner.

Slovenia’s Primož Roglič and The Netherlands’ Tom Dumoulin were five seconds down on Thomas, who now appears to have become Team Sky’s leader for the race.

Thomas had previously maintained he was riding in support of defending champion Chris Froome, but the four-time winner fell away on the final climb.

He ended 95 seconds behind Quintana and  gap to other rivals seeing him slip down from second to third in the overall standings.

"I didn’t know what to expect but it’s been a hard day and I’m happy to leave it behind," Thomas said.

"Chris told me with four or five kilometres to go that he wasn’t feeling great.

"There was no way I’d have attacked him but it made me understand that the others had to be in trouble too.

"I followed Roglič and Dumoulin and I went for the seconds bonus of the third place but I also got a time gap so it’s a nice bonus."

Thomas now leads the Grand Tour by 1min 59sec from Dumoulin, with Froome 2:31 down.

A largely flat 171km stage from Trie-sur-Baïse to Pau is due to take place tomorrow, with the final mountain stage coming the following day in Laruns.

The penultimate stage will be a 31km individual time trial in Espelette, before the ceremonial final stage in Paris on Sunday (July 29).