His team mate Chris Froome, who was hoping to hold all three Grand Tour titles at the same time, the Tour, Giro d'Italia and Vuelta a Espana, cracked on the final ascent up the Col de Portet and finished 1:35 down on the stage victor.
The Tour de France is the world's biggest and most iconic cycling race.
"I knew the last kilometres of the stage". "The riders' job is extremely risky, they are taking risks every day, people should not block the road, no matter what causes they are fighting for".
This means Tom Dumoulin moves into second place to split the two Sky riders, Thomas and Froome, on the podium.
Now here was a something that really was particular to French culture - the French love a protest, let's be honest, and particularly so during a Tour de France - but it was not directed at his riders.
"The road should remain free, we are not going to lock the riders in a stadium or on a tennis court", he said.
As the Tour reached the mountains of the Pyrenees, Philippe Gilbert and Alaphilippe led on the ascent to Col de Portet-d'Aspet.
Police were said to be arresting some protesters after farmers threw hay bales across the road before the peloton's arrival.
Philippe Gilbert's injured leg immediately after the 16th stage of the Tour de France
The descent is the same pass where Fabio Carsartelli crashed and died in 1995.
Four-time champion Chris Froome was among a large group of riders whose eyes needed treatment when police intervened to disperse farmers protesting funding cuts by disrupting cycling's biggest race.
Philippe Gilbert amazingly got back on his bike after this terrifying crash over a wall on Stage 16 of the 2018 Tour de France.
Alaphilippe also won the 10th stage and is wearing the polka-dot jersey of the mountains classification leader. It was fortunate they were only tossing hay bales into the road.
"I thought I was broken everywhere", said Gilbert, a teammate of Alaphilippe's on the Quick-Step team.
The last time a Tour stage was blocked by a demonstration was in 2004.
This stage was just 65km long, but featured three towering climbs between Bagneres-de-Luchon and Col de Portet.
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