Pogačar was on his limit for the final five kilometres of the Col du Granon climb to the finish, an unprecedented sight so far in the Slovenian's career as he failed to follow Vingegaard's move that saw the Dane win his first Tour de France stage and take the yellow jersey.
While he lost the maillot jaune, the 23-year-old still took the best young rider jersey on the podium after Stage 11, holding the classification by over eight minutes ahead of Tom Pidcock (INEOS Grenadiers).
So dominant in his appearances at the race so far, this scenario took a concerted effort all day from Jumbo-Visma to pressure and tire out Pogačar in a clinical display of tactics from the Dutch team.
"I don’t know what happened," Pogačar said after the stage.
"At the Galibier I was still so good. I got lot of attacking from Jumbo-Visma.
"Then, in the last climb I just didn’t have good legs. I suffered all the way to the end. It was not my best day. We will see tomorrow if I can do better."
Pogačar was targeted by Jumbo-Visma all day as they looked to use the first proper mountain stage of the race to put serious pressure on him.
And that strategy became very clear with 70 kilometres to go, when a group went clear with Pogačar, Vingegaard, Primož Roglič (Jumbo-Visma) and Geraint Thomas (INEOS Grenadiers).
The two riders from the Dutch team had Pogačar isolated, and each began to take turns attacking him, forcing him to burn energy latching back on to the wheel. Later in the race, Jumbo-Visma riders Christophe Laporte and Wout van Aert, who had been in the break up the road, came back down to assist.
Van Aert then led the yellow jersey group into the base of the Col du Granon, before Roglič also pushed the pace, with Rafal Majka the only teammate of Pogačar's to help him in the finale.
As the gradient and altitude climbed to the finish, Vingegaard went with 4.7 kilometres to go and neither Majka or Pogačar could respond allowing the Dane to gain a lead of two minutes and 22 seconds in the overall standings.
"Jumbo-Visma played it hard," Pogačar said.
"For us it was hard to control who went on the break. We were not many guys anymore. In the end, Van Aert and Laporte went up front. They played it great tactically today."
While he had a bad day, it was only the first in Pogačar's still very young Tour de France career, hard to remember due to how much he has already accomplished in the sport, and there's no doubt he can return to form as soon as tomorrow with the Alpe d'Huez summit finish awaiting the riders.
"I want to race and give everything from here to Paris," he said.
"I want to end the Tour with no regrets. It is not over yet.
"He (Vingegaard) got three minutes today; maybe tomorrow it’s me who gets three minutes. We will fight until the end."
The Tour de France continues with Stage 12, a special set-piece for the Tour de France with the summit finish to Alpe D'Huez on Bastille Day sure to bring out the best in the riders and fans. Watch from 8.55pm AEST on the SBS SKODA Tour Tracker and then from 9.30pm AEST on SBS and SBS On Demand.
