On his second flying lap in a wet Q3, Alonso set the fastest middle sector and was set to overhaul Nico Hulkenberg's surprise effort for second place, but was denied the chance to complete his lap when Oscar Piastri hit the wall at Turn 7.
This produced a red flag, that Alonso caught just as he was leaving the chicane before the start-finish straight, forcing him to abort his run late on.
But Alonso will start on the front row after Nico Hulkenberg was given a three-place grid penalty for a red flag infringement.
The Spaniard rued his apparent bad luck, also noting that he was moments away from setting a lap in Q1 before a red flag was waved when Zhou Guanyu's Alfa Romeo stopped in the opening part of the session.
"We've been unlucky generally with the red flags today and in Q1 also - I think it was one second to see the line and then the red flag came just in that moment. In Q3, it was I think four seconds before the crossing the line to be in the first row," Alonso said.
"I mean, we take it and I'm extremely happy [to be third] because it was a very complex qualifying to execute and you need constant communication with the team.
"Sometimes you feel things on the car, but then on TV or in the pitlane, there are different ideas. So you need that feedback with the engineer and the driver. It was a difficult day, but we have a strong chance [on Sunday] to score many points, so I'm happy now."
Asked to compare his efforts in Canadian Grand Prix qualifying to last year, where he qualified on the front row in a rain-affected session, Alonso explained that he had confidence in the car on both occasions to be able to perform.
He felt that pitlane positioning, particularly in this year's changeable conditions during qualifying, was of great importance and that Aston Martin being saddled with a pit garage further down the pitlane compared to its rival teams created another issue to overcome.
"Especially this year, the conditions were changing a lot and to position yourself at the end of the pitlane with the first couple of cars, I think it did help as well," he added.
"I think in this weekend, for example, we are in the wrong side of the pitlane, sometimes we took advantage being on the good side.
"So you know, all these details can make a difference when the conditions are changing so much. But I think confidence in the car is the key, and I had a lot of confidence this year and last year."
