Bottas was the first driver to drop into the 1:10 benchmark and set the new track record at the Circuit Gilles Villeneuve, but Vettel sent the Ferrari fans in the grandstand wild as he pipped the Finn by 0.081 to put himself on provisional pole.
He has raced in the F2 series the last two seasons and now sits 10th in F2 standings after eight races this year, including a third-place finish at Baku, Azerbaijan.
There's much more scope for overtaking in Canada than there is at most Grands Prix, so Hamilton could still get on the podium or better if he does well on Sunday, but he'll need to find the kind of pace his rivals displayed so readily here. "I will never do that".
When asked if he felt Red Bull had the pace for pole after seeing teammate Daniel Ricciardo go quickest in Q2, he said: "I knew we had a good vehicle, but I wanted to wait and see how competitive we would be in Q3". Mercedes was very quick, but I think we are not too far away.
"We had what looked like an electrical problem. I kept it off the walls, which isn't easy to do on this track". Obviously if something happens in practice then we will probably have to take one, but no is the answer today. "I guess I woke up the right way and what a day".
Hamilton leads Vettel by 14 points in the championship heading into the weekend, with Ricciardo third, 38 points off the lead. "The points are tomorrow".
Mercedes decided not to use the hyper-soft after bringing just five sets of the pink-striped compound to this weekend's race and will test the tyre for the first time in Montreal in final practice on Saturday morning. Then he turned in the leading performance in two 90-minute practice sessions at Circuit Gilles Villeneuve.
"We extracted the best we could out of qualifying". The impact damaged the nose of his auto, which has received a significant upgrade this weekend.
Earlier in qualifying, local favourite Lance Stroll failed to make it out of the first session and will start 18th.
Elsewhere, Romain Grosjean was unable to compete in qualifying as his engine went up in smoke just seconds after Q1 began, while there was more for Williams with yet another Q1 knock-out. He was just over a tenth of a second clear of the two Force Indias, which were split by just 0.007s in Esteban Ocon's favour, while Fernando Alonso rounded off the top ten for McLaren. "We've had some really tough luck".