Evenpoel who finished third overall in the Tour de France earlier this month, clocked 36 minutes and 12.16 seconds over 32.4km in driving rain to beat Italian Filippo Ganna by 14.92.
Another Belgian, Wout van Aert, won bronze.
"It means a lot. The Olympics are every four years so winning this time, I think at least I ticked that one off," Evenepoel, who will also be one of the top riders to watch in next weekend's road race, told reporters.
"It is amazing to beat those two legends of cycling."
Britain's Josh Tarling paid a heavy price for an early puncture as he took fourth place, 2.16 seconds off a podium finish.
Evenepoel set off like a cannonball and was the fastest at the first two check points as he rode with confidence on the wet roads of Paris.
Going into tricky corners with ease, Evenepoel, the 2022 road race world champion who will be one of the top riders to watch in next weekend's road race, never looked in danger and threw a punch in the air as he crossed the finish line.
By contrast, Ganna took risks on his way back to the Pont Alexandre III.
Riding a negative split - making a slow start and riding faster in the second half of the race - the Italian nearly hit a barrier but finished strongly to take Van Aert off the hot seat.
Asked what he could have done to beat Evenepoel, Ganna shrugged.
"I gave everything but him, he's a machine," he said, pointing to Evenepoel.
Van Aert had set the time to beat but eventually ended up more than 10 seconds behind Ganna, despite leading him by almost five seconds after 22km.
"It's my only talent, to ride a bike, so tonight I'm extremely proud," said Van Aert.
Evenepoel and Van Aert will team up in a formidable four-man squad also featuring Tiesj Benoot and Jasper Stuyven in next Saturday's road race, a 225-km ride in and around Paris.
"It's a completely different race, we have different cards to play. We're a team without only one leader. Wout is in great shape, Tiesj is an awesome rider and Jasper is a great one-day race rider," said Evenepoel.
"And there are other very good riders in the other teams."
