The double gold ensures Evenepoel's place in the pantheon of cycling greats and marks an impressive comeback four years after he plunged over a wall into a ravine during a race in Italy.
He is the only man to have ridden the Olympic double. Dutch cyclist Leontien Zijlaard completed the women's double at the 2000 Olympics in Sydney.
"So proud to win this and to be the first ever to take the double. It's history," said the 24-year-old Belgian.
Cheered on by massive roadside crowds, Evenepoel was clear leader when disaster struck.
The puncture sent him shuddering to a gut-wrenching halt less than 4km from the finish line, Evenepoel frantically waving his arms at his team as he waited for a replacement bike.
The team car arrived quickly and a panicked Evenepoel, unaware of the advantage he had on his pursuers, dashed over the remainder of the course to seal victory in front of the Eiffel Tower.
"I really feel sick from the effort, especially with that stressful moment with about 4km to go," he told reporters.
"The (team) car wasn't ready for that moment... but in the end I had enough time. What a day," he added.
'Really dangerous moment'
The race embarked from beneath the Eiffel Tower on a huge loop to the west of the city past the race track at Saint Cloud and the Palace of Versailles.
At 273km, the course was the longest in Olympic history, and the race was contested without team radios, which can reward a lone attacker as opponents find it difficult to organise a collective counter-attack.
Escape specialist Ireland's Ben Healey broke away solo with an early attack before Evenepoel bridged the gap to him inside Paris.
One of the pre-race favourites, Evenepoel then left his rivals for dead after attacking on a climb to Montmartre.
German rider Nils Politt received a huge cheer when he took a toilet break at the Deux Moulins cafe on the same climb.
Evenepoel rode solo over the final 15km of the race, eventually finishing well clear of French pair Valentin Madouas and Christophe Laporte, who took silver and bronze.
He got valuable support from fellow Belgian Wout van Aert, who led Evenepoel through the early action and then stalled rivals once his compatriot was clear.
His main rival Mathieu van der Poel of the Netherlands attacked on the first climb of Montmartre, but finished 12th, just ahead of British Olympic mountain bike champion Tom Pidcock.
"When Remco went, I knew it was a really dangerous moment. I'm happy for him," said van der Poel.
A series of well-timed advances made the difference for Evenepoel in a race that will go down as perhaps the greatest win of his career.
The Belgian star won the best young rider's award at his first Tour de France two weeks ago and said he partied so hard he stayed in bed for two days before dominating a rainy, crash-marred Olympic time trial on Saturday.
