It was his 65th career pole, tying Ayrton Senna for second all-time behind leader Michael Schumacher's 68.
Mercedes driver Lewis Hamilton was third, a third of a second slower than Vettel.
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.
The Red Bull driver made the most of a track that was ramping up to leap ahead of Bottas and finish fourth quickest, 0.393s off the pace. He was the one who inspired me to be where I am today.
The Senna family presented Hamilton with a race worn helmet from his childhood hero.
When asked if equalling Schumacher would mean as much, he said: I haven't got there so I can not really say.I can not really look that far ahead I have to be grateful and appreciate this moment. "To receive this and match him is a great honour".
Canada has proven to be a happy stomping ground for Hamilton in the past and so it proved again on Saturday following a thrilling qualifying session.
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Hamilton's second hot lap in Q3, a flawless and nearly breathtaking run and the fastest recorded at the circuit, was enough to secure pole and allay some of the concerns of the team, who have been working to better understand their car's performance. I'm shaking. Ayrton, I know for many of you was your favourite driver and he was for me.
Vettel had a mishap on turn two on his final fast lap or he may have had a chance to nip Hamilton for the pole.
Pressure has been mounting on McLaren's engine partner Honda to deliver on promised improvements to the power unit but none have been ready for Montreal and the team continues to languish down the timesheets.
Williams rookie Lance Stroll had a disappointing outing before a home crowd at his first Canadian GP.
"But in Q3 when it came to go to getting those last hundreds and thousands of a second, when I was pushing harder, the vehicle became more unstable again, not so easy to predict, so I struggled more with the auto today than Lewis did".
"It's been close in every race so far", said Vettel, a three-time F1 champion. Williams' Felipe Massa put in a strong run to pick up seventh place on the grid ahead of the Force Indias of Sergio Perez and Esteban Ocon.
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