Julian Alaphilippe dug deep to keep the overall Tour de France lead on Sunday as Simon Yates captured his second stage of this year's race and defending champion Geraint Thomas kept his title hopes alive after a late surge.

Few believed Frenchman Alaphilippe would emerge from two daunting summit finishes in the Pyrenees with the lead, but at the Foix Prat d'Albi finish he donned the yellow jersey for an astonishing 11th time as reward for his swashbuckling performances that have lit up this tour.

"I expected to lose a bit of time today. I'm delighted that I'm still in the yellow jersey. I gave my best to fight and retain the lead," said the 27-year-old world No.1 Alaphilippe.

"We knew it would be a hard day, I paid for my efforts in the finale," admitted Alaphilippe of the Deceuninck-Quick Step team who turned up at the Tour after multiple wins including the Fleche Wallonne and Milan-San Remo.

Thomas struggled on the final climb into the clouds, but then closed the gap on the leader to 1min 35sec by dropping him with a late burst afer initially looking like he was going to lose precious time on the overall leader.

"Tactics-wise, we were stuck a bit between a rock and a hard place, but the positive is that the legs responded a little bit better today. It was a decent day all round to be honest," Thomas said after the stage.

"I was suffering at times and the rest day will be welcome for everyone," added Thomas of Monday's second rest day before the Tour heads north towards the Alps for a final three days of high altitude reckoning.

Ineos sports director Nicolas Portal said the British team were "fine" with where they were so far.

"We're in second place with G (Thomas)" said Portal. "We were not expecting this from Alaphilippe, he's been imperious."

"It's exciting, he's the man of the tour so far, but there's a long way to go and we are hoping he blows," he said.

All Well At Ineos

Thomas singled out Thibaut Pinot for praise after the 2018 champion lost 49sec to the Frenchman.

Pinot, who won Saturday's stage and then left all the chief contenders behind him after attacking halfway up the Prat d'Albi 11km ascent, now stands only 15sec behind the Welshman.

"We'll have to really keep an eye on him now, we don't want to lose too much time to him. He's in great form, but look, he's not the only one," said the 33-year-old Ineos captain.

Thomas's co-captain, the 22-year-old Colombian Egan Bernal is now fifth, just 27sec behind his teammate.

"I lost time in the time trial and it changed nothing, yesterday he lost some time and it changed nothing and today again I moved closer. If I am going full gas at some point in the race for sure I will talk with him," said Bernal, who received high praise from sports director Portal.

"He's intelligent, he wants to win but he knows his place," said Portal. "He waited for G (Thomas) and G heard him talking to us on the radio and told him to go," he said, illustrating the two have a good understanding.

Sunday's stage winner Simon Yates also won Thursday's stage, also on a long distance breakaway, but his twin brother Adam's Tour de France chances look completely cooked as he lost time again.

Vuelta a Espana champion Simon said he had mixed feelings about his performance.

"I came here to help my brother Adam, and that hasn't gone to plan," he admitted after his twin had a poor time in the Pyrenees.

"But I had a second objective and that was to win a stage. I've now won two and who knows, maybe there's third one up the road," said Simon, who has told AFP he will target winning the Tour de France possibly in 2021 after going for gold at the Tokyo 2020 Olympic Games road race.