The 211km ride from Evaux les Bains to Le Lioran is the longest stage on this year's Tour, and while the expected early breaks materialised, it came down to the main contenders, with the overall top four making up the first four at the finish.
For Vingegaard, who came into this year's event having not raced for three months after suffering a collapsed lung and fractured rib, this was a significant victory over the race leader and favourite.
"It's of course very emotional for me," Vingegaard said.
"Coming back from the crash, it means a lot and all the things I went through in the last three months it makes you think of that and I would never have been able to do this without my family."
Slovenian Pogacar, twice Tour champion, still extended his overall lead to one minute six seconds over Remco Evenepoel, who finished third in the stage, with Denmark's Vingegaard a further eight seconds back in the general classification.
A group of 10 riders managed to get away for long parts of the race, but Pogacar's UAE Emirates teammates controlled the front of the peloton and never let a large gap open up.
Irishman Ben Healy was the last to resist before being swallowed up by the chasing pack with one kilometre left to the top of Pas de Peyrol, the toughest of the stage's six climbs, and Pogacar made his move close to the summit.
Pogacar extended his lead on the descent, but Vingegaard showed his mettle and left Roglic behind to go in pursuit of the leader, catching him just before the top of the next climb with less than 15km to the finish.
The final descent to the finish was a narrow ride, and Vingegaard took the lead on the home straight in a game of cat and mouse and when they finally started sprinting, he just held off Pogacar on the line.
"I couldn't follow the attack he had, it was a very, very strong attack, I just had to fight and actually I didn't think that I would be able to make it back," Vingegaard said.
"But I just kept fighting and I made it back and started relaying with him. A bit surprised I could beat him in the sprint."
Primoz Roglic came fourth after crashing close to the finish, but as it happened in the final three kilometres, he only lost 25 seconds on the leaders, the same as Evenepoel, rather than 55.
Pogacar and his team had done everything right, setting him up for the break, and he must have thought this would be a day when he put even more time between himself and his rivals, but Vingegaard had other ideas.
"It means so much to me. I'm so happy about the victory today, I would never have thought this three months ago," Vingegaard said.
