Vettel qualified second, but a slow start and contact with Max Verstappen at the first corner left him on the back foot, with damage not being spotted on his Ferrari SF70H until after an early safety auto period.
If it was plain sailing for the Briton it was anything but for Vettel who suffered front wing damage on lap one which forced him into an early pit stop and meant the Ferrari driver was playing catch up for the remainder of the race.
Daniel Ricciardo rounded out the podium after a tense battle for third.
The safety auto came out on the opening lap when, on the first turn, Romain Grosjean's Haas nudged Carlos Sainz's Toro Rosso, which plowed into the side of Massa's Williams.
Verstappen was running in second and holding onto the back of Hamilton's Mercedes when his engine died on Lap 11. The Spaniard, back in Formula One after his exploits at the Indy 500, made a trip to the grandstand to retire, throwing his gloves into the crowd before departing to the garage.
Bottas's podium finish this week puts him at 93 points this season.
A five-time victor at the Canadian GP, which celebrates its 50th anniversary, Hamilton already led qualifying but by just four one-thousandths of a second over Sebastien Vettel when he made his final trip around the circuit.
As such Mercedes are now back in charge of the Constructors' Championship, 222 points to Ferrari's 214.
TV replays showed that the fast-starting Verstappen, who later retired with technical gremlins, had nicked the nose of the Ferrari at Turn One, but the stewards took no action. Bottas locked up on entry to the corner to avoid hitting teammate Hamilton, allowing Verstappen to pass.
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And referring to the up and down nature thus far of the fight with Vettel and Ferrari, he added: "Maybe we won't need the rollercoaster ride so much!"
Sainz caused an opening lap crash with Massa, bringing out the safety vehicle, and will carry a three-place grid penalty over to the next race in Azerbaijan.
A bigger crash took Felipe Massa and Carlos Sainz out of the race just seconds later.
The incident ended both their days and brought out the safety car.At the restart Verstappen attacked Hamilton hard, nearly making a pass that would have changed the race.
It was the fastest qualifying lap ever at the Circuit Gilles Villeneuve, nearly 1.5 seconds faster than the pace that won him last year's pole and even one second better than Vettel ran in his Ferrari during Saturday morning's practice.
"I got a really good start, so I was generally in the clear", he said after leading from the pole to the checkered flag to earn his sixth victory on the Circuit Gilles Villeneuve - and third in a row. Magnussen collected a five-second penalty for passing Vandoorne while the virtual safety vehicle was deployed. Raikkonen was the first to pit on lap 17, followed by Ricciardo on the following lap and Perez on lap 19.
He finished 20 seconds behind his team-mate, having opted to do his final stint on softs, whereas Hamilton had gone for the ultra-soft compound. There was some discussion between Perez and Force India, telling him to let Ocon past - Perez didn't want to and Force India agreed to give him three laps to overtake Ricciardo before Ocon would try to overtake. Vettel then passed Perez on the penultimate lap for fourth.
"I could see on the TV screen that he was seventh, sixth, fifth, and then I saw him in fourth, and I was like "God damn it", it would have been better if he was in fifth".
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