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.
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 was the fastest at the first two check points as he rode with confidence on the wet roads of Paris, the Invalides military museum quickly fading in his rear view mirror when he set off like a cannonball.
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.
Van Aert had set the time of reference but eventually ended up more than 10 seconds behind Ganna despite leading him by almost five after 22km.
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.
