Seixas crossed the line 1,25 min ahead of Mattias Skjelmose, with Primož Roglič finishing just behind in third after the 164.1-kilometer stage from Pamplona to Cuevas de Mendukilo.
The young Frenchman had already claimed the leader's jersey after winning the opening time trial in Bilbao to become the first French rider since 2021 to win a WorldTour time trial.
The second stage was particularly steep, starting with Etxauri (2nd category, 6.6km at an average gradient of 6.6%), followed by two successive 3rd categories (Zuarrarrate and Aldatz) and, in the final, San Miguel de Aralar (1st category, 9.4km at an average gradient of 7.8%).
With 6.6km left of the climb, the 9.4km-long San Miguel de Aralar, with an average gradient of 7.8 percent, Seixas accelerated and broke away with ease. Matthias Skjelmose tried to take the wheel, but quickly resigned himself, as did Florian Lipowitz, Isaac del Toro, and Juan Ayuso.
At the top of the climb, Seixas had a 54-second lead with 19.5km still to go, including a descent and an uphill finish. While the Frenchman rode at full speed downhill, not hesitating to put his knee out to gain better angles and gain seconds on his pursuers, Mikel Landa was less fortunate as the Basque crashed heavily.
On the final final 8% steep climb, Seixas pushed on again to take victory 1,25 min ahead of Skjelmose and Primoz Roglic.
Seixas thereby extended his advantage in the overall standings to 1, 59 min ahead of Roglic, with German Florian Lipowitz another nine seconds further back in third.