29 July, 2018
Despite finishing around 9 minutes behind Alaphilippe, Thomas retains the yellow jersey, maintaining his 1 minute and 39 second advantage over teammate Chris Froome in general classification.
Thomas held an overnight lead of 1min 39sec on compatriot Froome, but took it to 2:31 after the four-time champion crossed the finish 1:36 behind Quintana and almost a minute off Thomas.
Tour de France director Christian Prudhomme condemned the actions of protesters who forced stage 16 of the race to be temporarily stopped as riders were caught in a cloud of pepper spray.
This year's Tour de France has been marked by a series of incidents on the sidelines of the race, including abuse directed at Team Sky and four-time champion Chris Froome.
While mountain stages in the Tour are traditionally more than 150 kilometers (100 miles) or longer - sometimes beyond 200 kilometers - this Tour features two legs that are relative sprints by comparison.
"I knew the finale was tricky", Alaphilippe said.
He told his following that: "As always I will come back stronger!"
Martin pushes himself up the Col de Portet
Froome is attempting to match the Tour record of five victories shared by Jacques Anquetil, Eddy Merckx, Bernard Hinault and Miguel Indurain.
With Thomas increasing his overall lead, the Colombian Egan Bernal finally showing the climbing aptitude that made his selection inevitable and Froome faltering, Team Sky's principal acknowledged that possibility.
He now trails his fellow Briton by 2:31 with three competitive stages left and Dutchman Tom Dumoulin sandwiched in between them. Riders with an outside chance of winning, or making it to the podium on the Champs Elysees, will, however, be tempted to blow up the race from the start, with Frenchman Romain Bardet, fifth overall and an excellent descender, the main suspect.
"In the last 200 metres I just thought I would go for the bonus seconds and get a little time gap as well", he said.
After the Tour's second rest day, the first drama of the stage came early on and from an unlikely source - the race temporarily neutralised after 29km because of farmers blocking the road with hay bales.
But the day belonged to Alaphilippe, who has spent the past 10 days chasing points to add to his collection for the King of the Mountains' polka dot jersey.
A breakaway of 47 riders took shape after the race was briefly interrupted by the farmers' protest.
"I had a bad kilometre between three and four to go and he pulled the gap out and I couldn't close in the end".
Harry Maguire, Anthony Martial, Willian
Leicester will improve Maguire's wages to around £75,000 in a bid to tie him down for another season but the Foxes are wary he could depart.
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