Defending champion Geraint Thomas was second while his Ineos co-captain Egan Bernal dropped down the overall standings and lost his best young rider’s white jersey finishing way off the pace.
Thomas dropped 14 seconds on the French overall leader to slip to 1min 26sec adrift in the general classification after the baking hot race-against-the-clock around the Pyrenean town.
“If he carries on like this he’ll win the Tour,” the 33-year-old Thomas said at the finish line.
The Welshman then told British broadcaster ITV that Alaphilippe’s barnstorming ride had taken him by surprise.
“He’s going incredibly well and is certainly the favourite or the one to watch at the moment,” he added.
“But there is a long way to go and a lot of hard stages to come.”
“I just wanted to keep the jersey, but to win the stage, on this form, is just totally amazing,” said Alaphilippe, the 27-year-old former soldier who is sending France wild with belief they can win a first Tour since 1985.
After the 80kph descent outside Pau with the sun making a strobe like flash effect as it flickered through the trees onto the blacktop, the packed holiday weekend crowds went wild as they realised Alaphilippe was keeping pace on the narrow hill roads outside the town.
As Alaphilippe made the 18 percent slope ahead of the home straight the noise was deefaning as the victory over time-trial specialist Thomas unexpectedly materialised.
Bernal finished 1min 26sec off the pace to drop down the rankings and lose his white jersey to Alaphilippe’s teammate Enric Mas.
France’s Thibaut Pinot was just behind these riders at 49sec, looking happy and relaxed.
It was also a good day for top five pretenders Richie Porte, Steven Kruijswijk and Rigoberto Uran.
There were gasps and cries of horror when Belgian rookie Wout van Aert fell in the home straight after getting caught up in the barriers and twisted his leg before being taken away in an ambulance.
Today’s stage 14 is a short 117km run over two Category 1 mountains with a summit finish at the fearsome classic Tour de France destination the Tourmalet, which some translate as ‘bad trip’ and which is the highest mountain pass in the Pyrenees.
Pinot and his FDJ manager Marc Madiot have vowed to gain revenge there for getting left behind in the crosswind at Albi.
“There’s a rage in him, and when the rage is on him he’s good, Saturday we roll,” Madiot told AFP this week.
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