The win is Vettel's 50th and only his second in Canada, after his 2013 triumph at the event. This early stop allowed Red Bull's Daniel Ricciardo to get ahead of him and Hamilton was never able to get close enough to pass the Australian late on.
On the basis of Friday practice, Sebastian Vettel does not see himself as a contender for victory even though Ferrari teammate Kimi Raikkonen set the second fastest time.
Vettel had failed to convert his previous two pole positions, in Azerbaijan and China, into wins.
I said yesterday how much this place means for Ferrari.
When asked if he was anxious errors could start creeping in as a result of an intense fight, he said: "I think you need to get the right balance between pushing development very hard, adding performance to the vehicle and at the same time keeping reliability". It means a lot. "I'm sure it's going to be on the way soon".
Canadian F1 Grand Prix 2018 Qualifying: Saturday's Results, Times, Final Grid
40 years after Gilles Villeneuve won his home race for Ferrari, his son Jacques drove his auto around the Montreal circuit before the race.
The race began in near-perfect conditions with an air temperature of 20 degrees Celsius and the track at 45 as the lights went out. Both cars were badly damaged but the drivers were uninjured.
When asked if Mercedes are confident they can get on top of their problems, Mercedes Team Principal Toto Wolff said: "I'm the opposite of confident". Having shown formidable race pace in the opening rounds Ferrari had been on the back foot to Mercedes but they brought an engine upgrade to this race which has put them right back in contention. Bottas was first to blink on lap 37, Vettel following one lap later, both going to super-softs.
It was left to Bottas to chase Vettel, who made a clean getaway from the start, with Verstappen nearly passing the Finn before the order settled down.
The only other retirement besides Stroll and Hartley was McLaren's Fernando Alonso who reported a loss of power due to an exhaust problem and was forced to garage his auto - a disappointing end to the Spaniard's 300th race.
Hamilton had gone into the meeting in Montreal with a 14-point advantage but leaves one point behind Vettel, a vast swing he would not have anticipated from one of his favourite circuits.
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