The Red Bull driver lapped the Montreal street circuit in a fastest time of 1min25.425 seconds with Britain's Lewis Hamilton second for Mercedes and Finland's Valtteri Bottas third in a Williams.
The German's pole ended a run of four in a row for Mercedes.
UNDERDOG RISES
The surprise of the session was the performance of Bottas, who posted the third fastest time ahead of the second Mercedes driven by Nico Rosberg.
Vettel's team mate Mark Webber and Ferrari's Fernando Alonso occupy the third row after an incident-packed qualifying in which the second session was red-flagged after Felipe Massa escaped unhurt after a crash.
Vettel, yet to win on the streets of Montreal, said: "I'm looking forward to the race tomorrow, I think we had a strong performance yesterday so whatever happens in terms of conditions it should be good.
"We expect dry conditions tomorrow, but it doesn't matter. We have both sets of tyres left, but even if it rains we should be in decent shape."
Hamilton, reflecting on his showing, said: ""I was doing a pretty good final lap but I ran wide, so it was unfortunate but I'm still happy."
Q3 from the F1 Canadian Grand Prix at Circuit Gilles Villeneuve
1. Sebastian Vettel (Germany) RedBull - Renault 1:25.425
2. Lewis Hamilton (Britain) Mercedes 1:25.512
3. Valtteri Bottas (Finland) Williams - Renault 1:25.897
4. Nico Rosberg (Germany) Mercedes 1:26.008
5. Mark Webber (Australia) RedBull - Renault 1:26.208
6. Fernando Alonso (Spain) Ferrari 1:26.504
7. Jean-Eric Vergne (France) Toro Rosso - Ferrari 1:26.543
8. Adrian Sutil (Germany) Force India - Mercedes 1:27.348
9. Kimi Raikkonen (Finland) Lotus - Renault 1:27.432
10. Daniel Ricciardo (Australia) Toro Rosso - Ferrari 1:27.946
11. Nico Huelkenberg (Germany) Sauber - Ferrari 1:29.435
12. Sergio Perez (Mexico) McLaren 1:29.761
13. Pastor Maldonado (Venezuela) Williams - Renault 1:29.917
14. Jenson Button (Britain) McLaren 1:30.068
15. Esteban Gutierrez (Mexico) Sauber - Ferrari 1:30.315
16. Felipe Massa (Brazil) Ferrari 1:30.354
17. Paul Di Resta (Britain) Force India - Mercedes 1:24.908
18. Charles Pic (France) Caterham - Renault 1:25.626
19. Romain Grosjean (France) Lotus - Renault 1:25.716
20. Jules Bianchi (France) Marussia - Cosworth 1:26.508
21. Max Chilton (Britain) Marussia - Cosworth 1:27.062
22. Giedo van der Garde (Netherlands) Caterham - Renault 1:27.110
1. Lewis Hamilton (Britain) Mercedes 1:27.649
2. Mark Webber (Australia) RedBull - Renault 1:28.145
3. Sebastian Vettel (Germany) RedBull - Renault 1:28.166
4. Valtteri Bottas (Finland) Williams - Renault 1:28.419
5. Nico Rosberg (Germany) Mercedes 1:28.420
6. Jean-Eric Vergne (France) Toro Rosso - Ferrari 1:28.527
7. Kimi Raikkonen (Finland) Lotus - Renault 1:28.667
8. Fernando Alonso (Spain) Ferrari 1:28.788
9. Adrian Sutil (Germany) Force India - Mercedes 1:28.799
10. Daniel Ricciardo (Australia) Toro Rosso - Ferrari 1:29.359
11. Nico Huelkenberg (Germany) Sauber - Ferrari 1:29.435
12. Sergio Perez (Mexico) McLaren 1:29.761
13. Pastor Maldonado (Venezuela) Williams - Renault 1:29.917
14. Jenson Button (Britain) McLaren 1:30.068
15. Esteban Gutierrez (Mexico) Sauber - Ferrari 1:30.315
16. Felipe Massa (Brazil) Ferrari 1:30.354
Q1 from the F1 Canadian Grand Prix
1. Sebastian Vettel (Germany) RedBull - Renault 1:22.318
2. Fernando Alonso (Spain) Ferrari 1:23.224
3. Mark Webber (Australia) RedBull - Renault 1:23.247
4. Valtteri Bottas (Finland) Williams - Renault 1:23.446
5. Felipe Massa (Brazil) Ferrari 1:23.735
6. Lewis Hamilton (Britain) Mercedes 1:23.801
7. Nico Rosberg (Germany) Mercedes 1:23.840
8. Nico Huelkenberg (Germany) Sauber - Ferrari 1:23.899
9. Jenson Button (Britain) McLaren 1:24.021
10. Jean-Eric Vergne (France) Toro Rosso - Ferrari 1:24.159
11. Sergio Perez (Mexico) McLaren 1:24.176
12. Esteban Gutierrez (Mexico) Sauber - Ferrari 1:24.408
13. Kimi Raikkonen (Finland) Lotus - Renault 1:24.451
14. Adrian Sutil (Germany) Force India - Mercedes 1:24.551
15. Daniel Ricciardo (Australia) Toro Rosso - Ferrari 1:24.770
16. Pastor Maldonado (Venezuela) Williams - Renault 1:24.776
17. Paul Di Resta (Britain) Force India - Mercedes 1:24.908
18. Charles Pic (France) Caterham - Renault 1:25.626
19. Romain Grosjean (France) Lotus - Renault 1:25.716
20. Jules Bianchi (France) Marussia - Cosworth 1:26.508
21. Max Chilton (Britain) Marussia - Cosworth 1:27.062
22. Giedo van der Garde (Netherlands) Caterham - Renault 1:27.110
Stay with Wheels24 for the 2013 Canadian GP weekend.