The Belgian rider's general classification hopes may be over after shipping 27 minutes on Friday's brutal climbs, but he responded in style to hold off France's Romain Bardet (32) after the two had broken away from a escape group on the Col Hourcere.
Bardet (DSM-Firmenich) stayed on the wheel of Evenepoel (Soudal Quick-Step) for the first half of the 9.5km climb to the finish but had no answer when the Belgian poured on the power with 3.5km remaining, winning by more than a minute.
Evenepoel's masterclass on the 156.5km route spanning the France-Spain border put him in firm control of the climbing standings as he scooped up stacks of points over the day's four categorised ascents.
The charismatic Belgian was emotional after crossing the line with his arms aloft, fighting back tears as he perhaps reflected on what might have been but for Friday's collapse.
Back in the peloton, the battle for the red jersey - now looking like being between Jumbo-Visma's powerhouse trio Sepp Kuss (28), Primoz Roglic (34) and Jonas Vingegaard (26) - was unchanged.
American Kuss retained the red jersey and his one minute 37 seconds advantage over three-times Vuelta winner Roglic while Vingegaard is 1:44 adrift.
The next best-placed in the standings is Juan Ayuso (20, UAE Team Emirates) who is 2:37 back on Kuss.
Evenepoel's horror show on Friday was completely unexpected but the way he bounced back was more predictable.
From the beginning of the stage he was in every attack and once the escape group became established it was clear he was the boss of it - making a tough day look like a breeze.
"Yesterday was a very difficult day and also the evening with a lot of negative thoughts in my head," Evenepoel said.
"Today I just woke up and thought 'Go for it and make the best of it'. I did a recon of this stage as I knew it would be important for the GC, and I knew perfectly how the climbs were, how hard they were.
"It was a super tough stage but really nice to take my second stage win. I think I can be very proud of this answer after yesterday."
Sunday's stage is a hilly route from Pamplona to Lekunberri.
