Pogacar was 39 seconds behind the leader Mathieu van der Poel at the start of the 5th stage in the west of Mayenne and made up much of the delay to move up to second place in the general classification.
The 22-year-old Slovenian mastered the 22.7 kilometer (14 mile) technical loop from Change to Laval to beat all the other main competitors in an impressive display of power and technical skill.
Pogacar was 44 seconds faster than last year’s runner-up Primoz Roglic while 2018 champion Geraint Thomas lost 1 minute and 18 seconds. Richard Carapaz, a former Giro champion with big Tour ambitions this year, was 1:44 off the pace.
“Today has been a very good day for me. I didn’t make any mistakes, ”Pogacar said.
Van der Poel has limited high mountain skills and is unlikely to remain in the mix once the race reaches the Alps later this week.
“I won’t keep (the yellow jersey) in the mountains, but I love Tadej, he’s a very nice guy and it’s really amazing what he does,” said Van der Poel.
Pogacar unleashed his power on the long stretches of flat roads and did not lose his rhythm on the hills scattered along the course.
Riding in aero position, Pogacar handled the tight corners of the technical final perfectly and completed the course in 32 minutes, at an average speed of 51 km / h (32 mph).
The UAE Team Emirates rider became the second youngest Tour de France winner last year after snatching the yellow jersey in a dramatic time trial on the eve of the arrival in Paris. He became the first rider to win two consecutive time trials on the Tour on Wednesday since Bradley Wiggins in 2012.
Van der Poel fought hard in the finals and put in his best time trial ever to retain the coveted yellow jersey, crossing the line exhausted with his mouth wide open.
Pogacar was 19 seconds faster than time trial specialist Stefan Kung. Jonas Vingegaard was third, 27 seconds behind.
In total, Pogacar is eight seconds behind van der Poel.
Time trial specialist Tony Martin, Roglic’s teammate at Jumbo-Visma, was among the first to start. Under gray skies but dry roads, the four-time individual time trial world champion played it safe after his big crash earlier in the race and crossed the finish line in 35 minutes and 33 seconds.
Mikkel Bjerg of Denmark, a rising star in the discipline with three U23 titles in the time trial, significantly improved Martin’s time with 33:01.
Bjerg finished his race in a light drizzle and the rain intensified afterwards, making the roads slippery for the riders who started later. American Brandon McNulty was among them and crashed, crossing the finish line far behind and with both legs bloodied.
Times improved once the rain stopped and the roads dried up. Five-time Swiss champion Kung stayed in the hot seat for a while and looked dejected when Pogacar crossed the finish line.