Alaphilippe now holds a four-second lead over Roglic with Pello Bilbao (Astana) at 29 seconds and the majority of pre-race favourites a further four seconds in arrears. The win is Alaphilippe's first on European soil since his Vuelta a Espana victory last year and the 22nd of 2018 for QuickStep-Floors.
"I am very happy, especially as I got sick after Milano-Sanremo and had to rest before returning to training. I was very motivated after this small setback, so I worked hard to be back at my best," said Alaphilippe. "The plan was to take a stage here and even though we did a recon of the final climb yesterday and on paper it suited me, I didn't know how my legs would react following that break.
"I was focused, smart and strong, I worked well together with Roglic, who too was very strong, and in the end I bided my time before powering to this nice win. A big thanks to my team for protecting me today and to the amazing crowds, who cheered for us before the start and at the finish."
Alaphilippe started his season with a stage win at the Colombia Oro y Paz and then placed fourth overall at the Abu Dhabi Tour. The leader's jersey is his first of the 2018 season with a moustache also a new look. And the facial addition is here to stay as the 25-year-old explained.
"Everyone in the peloton asked me what was with the moustache. After my teammates the other day, now the other riders came to me and asked if there was any reason behind this new look. To be frank, there wasn't any and I wasn't even focused on it, but now that I won, I'll keep it," he said.
There was further cause for celebration at the QuickStep-Floors bus with Enric Mas crossing the line in fourth place and taking the best young rider classification. The team now leads all bar the mountains classification with Jonathan Lastra taking the polka dots.
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For Mas, the result is his best yet of the season and despite the result and performance, the 23-year-old explained he isn't yet thinking about the general classification.
"The stage wasn't easy and the peloton grew nervous as the last climb was approaching," said Mas. "Everyone knew there will be fireworks there and battled for a good position. I was at all times attentive and at the front, together with Julian, as I felt good throughout the day and knew it was important to be up there with the strong crosswinds. At the end, I came just outside the podium, but the way my legs responded satisfies me. I lead the youth rankings and the confidence is there, so now I'll just take it one day at a time and see what this race brings in the next stages."
Stage 2 of the Vuelta al Pais Vasco is 152.7 kilometres from Zarautz to Bermeo. The San Pelaio climb inside the final 10 kilometres of the stage is likely to trim the bunch for a reduced sprint finish with Alaphilippe's hold on yellow set to last until at least the stage 4 time trial.
