Less than 30 kilometers into the stage, a protest by French farmers brought to the riders to a halt after bales of hay were thrown onto the road.
French police forces dispersed the demonstration by throwing tear gas before riders arrived, according to Tour de France broadcaster France Televisions.
It was in the same descent that Italian Fabio Casartelli crashed and died in the 1995 Tour de France.
The race restarted around 15 minutes later.
Four-time race champion Chris Froome was also seen putting teardrops in his eyes.
Froome sits second in the general classification, 1 minute, 39 seconds behind Sky teammate Thomas.
Mitchelton-Scott's Yates led on the descent into Bagneres-de-Luchon after attacking three kilometres before the summit of the Col du Portillon, cresting the mountain with a 22-second advantage.
Great Britain's Geraint Thomas cleans his eyes after tear gas was used during a farmers' protest, which attempted to block the stage's route.
French farmers bring Tour de France to standstill with protest
Belgian rider Philippe Gilbert was leading when he crashed earlier in the stage while descending from the Col de Portet-d'Aspet, hitting a wall and flipping off his bike spectacularly.
"I was not affected because I was not in the first 10 of the group", he said.
It was a gift, but Alaphilippe didn't care as he cruised to his second stage win of this year's Tour.
Martin came in 28 seconds behind him and Thomas finished third a further 19 seconds back to single himself out as Team Sky's leader.
Their field is the road, the road is open - we can not lock them in a swimming pool or a stadium or in a tennis court. They must be respected, they take enough risks for their job.
The last time a Tour stage was blocked by a demonstration was in 2004.
Quick-Step bosses panicked when Gilbert went over the wall - it was on the same descent, albeit several kilometres below, that Italian Fabio Casartelli died in a disgusting crash in 1995. "It's bike racing", the Frenchman said.
Stage 17 is a 65 km trek from Bagneres-de-Luchon to Saint-Lary-Soulan on Wednesday.
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The bundled DUALSHOCK 4 wireless controller is also painted red to match the console and comes with white dials and buttons. The bundle includes a Spider-Man themed PS4 Pro console, DualShock and a copy of Insomniac's Spider-Man game .