The Briton had been clear favourite to grab the top spot on Saturday, but could not put together the perfect lap he needed to overhaul his German rival.
Hamilton said he had to take full responsibility for what happened.
"I just had two laps and I didn't do good laps," he explained. "It was nothing to do with the car.
"Small things make the difference all the time, especially when we have the same car, and Nico is very, very quick and performing well.
"On my first lap I got traffic, but the second lap I was on my own and just didn't do a great lap.
"Out of all the qualifying session I have done, I think most of them have been good laps."
With overtaking difficult at the Circuit Gilles Villeneuve, Hamilton admitted that overhauling his team-mate would be tough on Sunday.
"I think strategy is going to be the real opportunity tomorrow," he said. "The start is an opportunity but we have got the same starts, and he is on the cleaner side so we should hopefully go away in our positions.
"And then after that it is really just looking after the tyres."
Although much has been made of Rosberg grabbing pole position at a track that Hamilton has done so well at in the past, the German said there was no greater significance to his effort than it putting him in a great place for the race.
"It's extremely satisfying, definitely," he said. "Of course you are all saying it is Lewis's track, but it is not something I think about in that way.
"It is a track that I enjoy myself, it is an awesome track and if I get everything right I know I can do it. It doesn't give me extra pleasure because he has a good statistic here; pole position is awesome for tomorrow."
And he admitted that he was not unduly concerned about Hamilton using strategy to try to overhaul him.
"Worried, no. But aware that it is going to be a good fight, yes," he said.
"We knew internally that qualifying is quite decisive here this weekend because there is not much you can do here strategy-wise when you are fighting the same car."
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