The defending champion dominated the eight-kilometre climb at 7.9% to clock 23 minutes and beat Denmark's Jonas Vingegaard by 36 seconds, with another Slovenian, Primoz Roglic, taking third place 1:20 off the pace.
Belgian Remco Evenepoel hung on to third place overall by the skin of his teeth following a disappointing effort that saw him finish 2:39 behind Pogacar.
After his fourth stage win in this year's race, UAE Team Emirates - XRG rider Pogacar leads Vingegaard by 4:07 and Evenepoel by 7:24.
German Florian Lipowitz showed great form again and trails Evenepoel by six seconds.
Pogacar picked a regular road bike for the solo effort against the clock while Evenepoel and Vingegaard opted for a time trial bike - heavier but with better aerodynamics.
It was quickly clear that, regardless of those calculations, Pogacar was again the strongest rider as he posted the best time on the brief flat portion ahead of the main ascent before further extending his advantage.
"I'm super happy. This time trial was a question mark for me back in December. I wanted everything to be perfect, and the team delivered - everything was on point," he told reporters.
"I was targeting to go all out from start to finish. I almost blew up at the end, but when I saw I was going to win at the finish, it gave me an extra push."
The 26-year-old said it had been a close call between the road and the TT bike, but in the end he chose the most comfortable ride.
"The biggest decision was which bike to ride today. Obviously, we ride road bikes all year round, but we did the calculations and the time ended up about the same. So I decided to go with what I felt more confident on."
Pogacar went full gas from the start. "My tactic was simple: go all out from the bottom to the top," he said. "At the first time check, I saw I was five seconds ahead - that gave me confidence. The second split was even better," he explained.
"Basically, I was trying not to blow up in the first part. I almost did in the end - maybe in the last kilometre. From 3 to 2 km to go, I reset a bit because that last kick is super steep."
Pogacar will now go for a hat-trick of stage wins on Saturday, when the 14th stage will take the peloton from Pau to Luchon-Superbagneres with the awe-inspiring climbs of the Col d'Aspin, Col du Tourmalet, Col de Peyresourde before the final ascent, a 12.4-km effort at 7.3%.