Pogacar, 22, is the youngest rider to wear the overall leader yellow jersey at the end of the race for two years in a row.
The United Arab Emirates The rider also won the white jersey for the best U-25 rider and the polka dot jersey for the mountain classification after a dominant performance throughout.
Danish Jonas Vingegaard took second place overall with Ecuadorian Richard Carapaz in third place.
Pogacar is now heading to Tokyo for the Olympics, where he will be among the favorites for next Saturday’s road race.
After a procession ride to Paris, multiple attacks occurred on the eight laps around the finish line on the Champs-Elysees, with Mark Cavendish’s Deceuninck-Quick Step team controlling the gap.
The Briton, however, did not benefit from his usual leader, Mikael Morkov, and Van Aert clinched victory for his third stage win on this year’s Tour.
Belgian Jasper Philipsen was second ahead of third-placed Cavendish, who won the green jersey for the points classification for the second time, having won four stages this year.
Van Aert, who will be taking part in the time trial in Tokyo, won Saturday’s individual time trial after also winning a mountain stage with two ascents of the dreaded Mont Ventoux.