At the end of the 21st stage, Pogachar covered a total distance of 3414.4 km in 82 hours 56 minutes 36 seconds.
The Slovenian also won the mountain (107 points) and youth competitions.
Second place in the general classification was taken by Jonas Wingegaard from Jumbo-Visma, 5 minutes 20 seconds behind the winner.
The Ecuadorian Richard Carapaz, representing INEOS, closed the top three with a lag of 7 minutes 3 seconds.
Briton's Mark Cavendish of Deceuninck - Quick-Step won the race points with 337 points.
The team event was won by Bahrain Victorious.
Earlier it was reported that Wout van Art won the final stage of the Tour de France.