Hamilton was fastest in Friday's early practice, but damaged his vehicle when he hit the wall in the afternoon.
"I struggled with the vehicle, with the set-up maybe." he said after qualifying.
The Englishman may have been boosted by a new Mercedes engine this weekend, but he was unable to live with the speed of Vettel's Ferrari on the long back straight - the German doing the damage in the final sector to beat Hamilton by two tenths.
"I want to change that, with the FIA, and in the teams and the mechanics and in the media, too", he said. We're very quick down the straights, not so easy to pass but we will see, it's a long race. I think just over a tenth from third.
Hamilton said there were still humps along the way, but he had developed the "tools to handle and deal with them" and was now "in the best place I've ever been".
Mercedes have dominated the campaign so far, finishing first and second at all but one of the opening six rounds.
Despite missing out on pole, Hamilton still starts tomorrow's race on the front row and will be ahead of Charles Leclerc on the second row, meaning that all is still to play for.
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"I struggled today in Q3".
"I hope this is a turning point for them and it's going to be very close from now on and we're going to have a serious battle throughout the season". The two men were evenly matched until final qualifying, only for Leclerc to fall away while Vettel channelled the spirt of his dominant Red Bull days to produce a lap for the ages. "Tomorrow will be a different experience and I hope I have the (car) set-up right for it".
"That is as much realism as you can get."Vettel won from pole position in Canada a year ago and Mercedes has suggested the high-speed circuit could again favor Italian rivals whose season has yet to get into gear".
"It's very bumpy, very rough".
Ferrari delivered a first surprise at the Canadian Grand Prix on Friday by posting the quickest lap times during the afternoon practice session.
"We are definitely in the fight", said Stroll of the competitive midfield.
Red Bull's Max Verstappen spent much of qualifying complaining to his pit about traffic and a lack of grip but was ultimately undone by a bad break when Haas's Kevin Magnussen crashed in front of him and did not complete a flying lap that had looked good enough to but him into the third round.
Montreal native Lance Stroll ended up 10th in his Racing Point, 0.994 seconds behind the pacesetter and three spots behind teammate Sergio Perez.