After the requisite breakaway was consumed by the peloton, Alaphilippe (Quick-Step Floors) blew the 166.7km stage apart on San Pelaio, the 3.3km-long climb averaging 8.1 per cent before sprinting from a four-man group to the victory in Bermeo.
As on Stage 1 Primoz Roglic (LottoNL-Jumbo) was again second with Gorka Izagirre (Bahrain-Merida) third.
Alaphilippe now holds an eight-second lead over Roglic in the general classification, with Izagirre at 39 seconds in third.
“The stage was on from the start and the crosswinds made it even more brutal," Alaphilippe said. "But, fortunately, I have a great team around me, who set an incredible pace at the front of the bunch, keeping the attackers on a leash, and a very strong Enric [Mas], who played a big role in my victory.
"Unlike yesterday, I had no idea on the final, but stayed calm and confident in my legs and sprint. Despite taking some more bonus seconds and increasing my advantage in the GC, I’m not changing my goal and will continue to take it day by day.”
The race continues with a 184.8km stage from Bermeo to Valdegovia.