He finished more than a minute ahead of the Dane and nearly 3 minutes ahead of the other main title contender, Remco Evenpoel of Belgium.
It was arguably the toughest stage of this year's race, with five categorised climbs - four of them Category 1 ascents, and the Category HC finish itself.
It's Pogačar's third stage win at this year's Tour de France and the 80th victory of his professional career.
Tomorrow is a rest day ahead of a flat stage from Gruissan to Nimes on Tuesday.
The race finishes with an individual time-trial in Nice next Sunday.
It caps an excellent weekend for Pogačar and his UAE Team Emirates teammates.
He's hoping to become the first man since 1998 to win the Giro d'Italia and Tour de France in the same season, a feat which has only been achieved by seven riders in the history of the sport.
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