Pogacar won six stages as he reclaimed the Tour title from two-time winner Vingegaard last year and is now up to 21 in total.
He is now sixth on the all-time list, with Sir Mark Cavendish having set the record of 35 last year, and there are still eight stages remaining on this year’s edition.
“I’m super happy,” said Pogacar. “This time trial was quite a big question mark already in December for me. I wanted everything to be perfect.
“I was really targeting to go from start to finish all out and tried to smash it as much as possible on the pedals.
“I almost blew up in the end but I saw the timer at the top and it gave me an extra push because I saw that I was going to win.”
Australian time-trial champion Luke Plapp set an early benchmark and his time stood for most of the day as riders struggled on the punishing finish.
The 8km climb to the line had an average gradient of 7.8% but the final 300m were 16%.
The riders were sent off at two-minute intervals, and after shipping 2mins 10secs to Pogacar on Thursday, Vingegaard managed to catch Evenepoel 50m from the line.
“Yesterday was probably one of my worst performances but today was one of my best so it’s nice to come back like this,” said the Dane.
Vingegaard and Evenepoel were among a handful of riders that chose to go with adapted time-trial bikes but Pogacar, who opted for a road bike, was quickest at each of the two time-checks before powering up the final section.
After a gruelling mountain stage on Thursday, the peloton is set for another on Saturday along a 182.6km route from Pau to a summit finish at Luchon-Superbagneres.