The Olympic Champion suffered a loss to the world champion in Quebec two days earlier but this time had all the answers on the punchy 205.7km Montreal circuit. Diego Ulissi (Lampre-Merida) finished third and Australia's Michael Matthews (Orica-BikeExchange) managed fourth.
"I came here many times and I had not managed to win yet, van Avermaet said. I'm very happy I've done it.
"We worked very hard with [Julian] Alaphilippe and [Peter] Vakoc in the finale to try and catch Rui Costa and I'm glad we made it so that I had could have my chance to go for the win.
"It's been an incredible year. For many years I was the guy who didn't quite make it and now I've won all those great races. I hope I can continue like this and win races like Flanders or Paris-Roubaix.
"It's sure that Peter and I have responsibilities as the world champion and Olympic champion and I'm sure we will continue to do our best in the years to come."
After a series of race long attacks and collective breaks were neutralised, the major battle started on the last ascent of Camilien-Houde when Ryder Hesjedal (Trek-Segafredo), Romain Bardet (AG2R La Mondiale) and Costa (Lampre-Merida) attacked.
Costa then went out on his own for the last five kilometres before being reeled in with a single kilometre to go.
Alberto Bettiol (Cannondale-Drapac) was the next to chance his legs but van Avermaet was the man who crafted the victory after Sagan left his effort a little bit too late.
I'm happy. First in Quebec and second in Montreal is not bad," Sagan said. "What happened? I was just tired.
"I had cramps in the final sprint and I could not sprint better so I'm content with my second place. I cannot think about the world championships yet. It's too far away."
