Pogacar, who had already won stage 2, finished 17 seconds ahead of Italian time-trial specialist Filippo Ganna and two minutes in front of his great rival, Welsh rider Geraint Thomas.
The UAE Team Emirates team leader is now 2min 36sec ahead of Colombian rider Daniel Martinez in the overall standings.
"I prepared well for this time trial and worked a lot on the time trials, my position on the time-trial bike," said Pogacar.
After Ganna set a testing time of 52:01 all eyes were on Martinez, who began the day 47sec off the lead, Thomas, who was one second ahead of him, and Pogacar.
While Thomas, who turns 38 on May 25, and Martinez struggled to chew up the tarmac between Foligno and Perugia, Pogacar shifted into overdrive clocking 51.44 at an average speed of 47.1 km/h.
Only 11th at the halfway point, 44 seconds behind Ganna, Pogacar finished very strongly indeed, taking advantage of the last six kilometres of uphill sections to knock out the competition.
"I remained cautious until the last climb when I gave it my all," he said.
Martinez (Bora) was eighth quickest on the day but gave up 1:49 to Pogacar. He did, however, move up to second place in the GC with a 10-second advantage over a weary Thomas.
"I got stuck," said the Welsh Ineos rider who won the Tour de France in 2018. "I gave it my best shot, but I was having a bad day."
Saturday's 8th stage, which concludes with a fearsome final 14km climb to the finish at 1452m altitude, could enable Pogacar, a keen climber, to extend his lead even further.
The Slovenian, who is taking part in the Giro for the first time in his career, is aiming to become the first rider since Italy's Marco Pantani in 1998 to win both the Giro d'Italia and the Tour de France in the same year.
