The Frenchman not only maintained his overall lead after the 27.2km stage, but extended it. He finished 14 seconds ahead of Thomas in second place and 36 seconds ahead of Rigoberto Urán (EF Education First).
Alaphilippe now leads by 1-26 over Thomas, the defending champion, as the Tour de France faces its first high-altitude summit finish tomorrow up the Tourmalet.
"Yeah, for sure the way he's riding," Thomas said of Alaphilippe's threat to the eventual overall title.
"If he can keep that up then he'll win. But there's a long way to go and a lot of hard stages to come."
Stage 14 climbs to 2,115 metres to finish on the Tourmalet tomorrow. Stage 15 then climbs several passes before finishing at 1,194 metres at the Prat d'Albis.
Alaphilippe completed his ninth day in yellow and raises a red flag for the other contenders. If rival teams including Ineos, with their owner Jim Ratcliffe arriving today, do not drop him tomorrow then they truly must be worried for the Paris finale.
Alaphilippe won Strade Bianche, Milan-San Remo and Flèche Wallonne this spring, but his biggest stage race wins remain the 2016 Tour of California and the 2018 Tour of Britain.
Thomas felt the heat on the course today, but managed himself well to finish above all of his other rivals. "Not too bad," was Thomas' evaluation of his ride.
"I just felt like I was overheating a bit. I was trying to deal with that. That's not an excuse, it was OK. Yeah, just felt like on that last bit I didn't really.
"Yeah, I think so [that I could open up the cylinders today]. I felt just like it was controlled.
"Then in the last 8km or so when I felt like I really wanted to step on it, I didn't quite have that last 5 per cent, but it was still a decent ride, but you always pick apart a TT."
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