Charles Leclerc came out on top with a time of one minute, 12.177 seconds, edging teammate Sebastian Vettel by 0.074 seconds.
Vettel won from pole position in Canada previous year and Mercedes have suggested the high-speed circuit could again favour Italian rivals whose season has yet to get into gear.
Afterward, the Ferrari driver, who hadn't won a pole in the past 17 races, explained his enthusiasm.
"This is nothing that's not been spoken of before", said Hamilton, who conceded their relationship had "not always been great" before adding it was "fantastic now". But this year Ferrari have had the quickest vehicle in a straight line, even if their advantage hasn't been as pronounced during the races.
"I'm very happy for the team".
"You know what, the feeling in the auto when it just keeps coming and the feeling - it felt so good". "How you stop that, that is definitely a part of the regulations but I think on a more global scale, I think there need to be some more changes outside of the regulations in my opinion". "All in all, a good day where we put in a lot of laps around a really fun race track; I like it here!"
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But in Hamilton he has a formidable Canada rival - the Briton has six wins, making it the joint-most successful race of his career along with China, Hungary and the United States. "Sometimes you do these races and I could probably do two or three races in a row and Formula One should not be like that". The field is very tight.
Valtteri Bottas in the second Mercedes was third, with the McLaren of Carlos Sainz and Haas of Kevin Magnussen in fourth and fifth.
Ferrari delivered a first surprise at the Canadian Grand Prix on Friday by posting the quickest lap times during the afternoon practice session.
As for Stroll, his immediate goal will be to emerge from Q1 - the first round of qualifying - on Saturday, something he has failed to do in the last 10 tries dating to last season.
"This is one of the tracks where you need to dare going very close to the walls in numerous places", he told the post-qualifying news conference.
"It's a bit weird now, I don't know what to say".
Red Bull's Max Verstappen, who complained to his team during the morning session that the track was "insanely dirty", introduced himself to the infamous "Wall of Champions" in the second, slapping the barrier with his left front tire. That forced him to revert to an older-spec engine for qualifying and Sunday's race.