A wide line on the final corner from Colombian sensation Sergio Higuita (EF Education First) proved enough of a slip up for Pogačar to take advantage, accelerating underneath and holding his rival off for the stage win.
With the victory, Pogačar also took on the leader's yellow jersey, after previous wearer Tejay van Garderen (EF Education First) dropped off earlier in the stage.
"It was for sure team effort, once again my team did a really good job protecting me leading me out final climb.
"I just did my best in the last five kilometres or six. I was going really well today."
Pogačar had to counter a late attack from Higuita, who sat only 12 seconds behind the Slovenian coming into the stage and threatened to take the stage win and with it the overall Tour lead.
"When I got to Higuita, I slowed down as George Bennett (Jumbo-Visma) was coming but was not so much a threat to me so I was waiting. I started my sprint behind Higuita, he made a mistake in the last corner and I went faster than him. It was really good."
With pre-race favourites like van Garderen, Gianni Moscon (Team Ineos) and Kasper Asgreen (Deceuninck-QuickStep) faltering as the pace hotted up on the climb, the stage came down to a battle in four.
Richie Porte (Trek-Segafredo), Pogačar, Higuita and Bennett jumped away in the final four kilometres of the ascent of Mt Baldy. Surges from Bennett and Porte brought the quartet level with attacker Maximilian Schachmann (BORA-hansgrohe) before Higuita launched a massive attack that looked to distance the remaining contenders.
Porte dropped back with a slipped chain, but recovered to fight back to be nearly on terms at the finish, while Pogačar slowly ground up to the Colombian's lead. Making contact within the final kilometre, Pogačar then sat on the wheel, as Higuita needed a gap in addition to the bonus seconds to bridge the 12 second deficit that Pogačar held over him.
Higuita took a poor line on the final corner, running wide and allowing Pogačar to come up the inside and take the victory.