The triple Formula One world champion will be favourite to win in Montreal for the fifth time on Sunday, knowing he can retake the title lead if Rosberg draws a blank. The German is 24 points ahead after six of 21 races.
Hamilton's love affair with the Circuit Gilles Villeneuve, where he took his first pole in 2007, continued as he lapped with a fastest time of one minute 12.812 seconds and beat Rosberg by 0.062.
Rosberg's second place brought him a 13th consecutive front row start, with Ferrari's Sebastian Vettel third fastest and 0.178 behind Hamilton.
"It actually wasn't a great lap," said Hamilton.
"I didn't have the same pace I had yesterday, but it was obviously enough," added the champion, who dominated Friday practice, after his 53rd career pole. "It doesn't matter how far you are ahead as long as you are ahead.
"Ferrari have picked up the pace with the upgrades they have brought. It will be exciting to have a race with them."
Two weeks after lucking into his first win of the season in Monaco, thanks to a Red Bull pitstop bungle, Hamilton provided further evidence that his campaign is fully back on track.
Australian Daniel Ricciardo qualified fourth for Red Bull, with 18-year-old team-mate Max Verstappen fifth and Kimi Raikkonen sixth for Ferrari.
EVERYTHING POSSIBLE
Rosberg has never won in Canada, finishing runner-up for the past two years, but he refused to rule out his chances of a first win in three races.
"Everything is still possible," said the German, who won the season's first four grands prix. "The weather is all over the place and from second place on the grid everything is possible. I will still try and go for the win."
Vettel apologised to his team after missing out on pole, and also skimming the wall at the last corner, saying: "Going into qualifying I thought it was possible. As a driver you always think there is more.
"I am happy with the step we have made. I brushed the 'Wall of Champions' so I don't have to do that again."
Fernando Alonso will start 10th after Spain's two-time world champion signalled McLaren's steady if unspectacular progress by reaching the final qualifying session for the third race in succession.
Compatriot Carlos Sainz brought out the red flags in the second phase when his Toro Rosso hit the feared wall. He qualified 16th but will move up a place thanks to Daniil Kvyat's three place penalty carried over from Monaco.
Danish driver Kevin Magnussen did not take part in qualifying with Renault unable to repair his car in time after a crash late in final practice.
Qualifying brought more disappointment for Renault, with British rookie Jolyon Palmer missing the cut in 17th place by a whisker.
Rain also made the track very greasy, and Manor's Indonesian driver Rio Haryanto ended up in the barriers.
(Editing by Alan Baldwin)
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