The current world champion qualified ahead of Mercedes’ Lewis Hamliton but Williams’ Finnish driver Valtteri Bottas secured a surprise third place at the Circuit Gilles Villeneuve.
Q1 began with light rain and though all cars went out on super-soft tyres to test track conditions, the circuit was too wet and intermediates were fitted.
As the cars found some pace, Red Bull’s championship leader Vettel went quickest with a 1:22.318 ahead of Alonso and team-mate Mark Webber.
There was disappointment for Force India’s Paul Di Resta who went out along with Charles Pic, Romain Grosjean, Jules Bianchi, Max Chilton and Giedo van der Garde.
Rain continued in Q2 and slowed the lap times down, Hamilton setting the early pace with 1:29.259 before Mark Webber set a 1:28.145.
Felipe Massa crashed out at turn three, causing a red flag with just under two minutes of Q2 to go as the stewards moved his car from the barriers.
The remaining 15 cars took to the track for another lap, Hamilton setting the quickest time after the restart with a 1:27.649.
Surprise inclusions into Q3 included Bottas and Toro Rosso pair Daniel Ricciardo and Jean-Eric Vergne.
Vettel was looking for his third successive Canadian Grand Prix pole and set a 1:25.425 ahead of Hamilton and Bottas.
The session’s climax saw the track get slower due to more rain, with no-one able to improve their time and Vettel secured his Montreal pole position hat-trick.