In pursuit of his fourth Canadian Grand Prix victory, Hamilton will start from second on the grid at the Circuit Gilles Villeneuve for the third consecutive race this season.
On this occasion it will be Red Bull's Sebastian Vettel ahead of him rather than Mercedes team-mate Nico Rosberg who had claimed the last three poles prior to today.
Hamilton did have a shot at top spot as he was on course to topple triple world champion Vettel on his final run in the dying moments of what was a crazy qualifying given the drizzly conditions.
But with very light rain falling again in the final sector, Hamilton momentarily locked up into the penultimate corner and the opportunity was lost.
"I was doing a pretty good lap, I was six or seven tenths up, but I went wide," Hamilton said.
"I'm still really happy for the team. It's good to be on the front row, which improves the chances a bit, but it's going to be a tough race tomorrow [Sunday].
"Obviously Sebastian is very quick, the Ferraris have been quick on their long runs here, so I guess it really depends on the conditions.
"At the end of the day I've got to do the job, but as you know I love it here, it's a great crowd - even though the weather was not so great today.
"I'm sure there will be plenty more people tomorrow [Sunday], so let's hope we can put on a good show for them."
The drizzle struck shortly before the start of qualifying, forcing an abandonment by some of a hoped-for dash on the supersofts as they had to swiftly switch to the intermediates more suited to the damp track.
As the drizzle came and went throughout, fortunes fluctuated for many on track, with Vettel ultimately holding his nerve to claim the 39th pole of his career.
It is Vettel's third consecutive pole for this race, although on the past two occasions he has failed to win, losing out to Jenson Button on the last lap in 2011 and to Hamilton last year.
"It was obviously very tricky throughout," said Vettel.
"In the end it was very tight with Lewis, but I'm extremely happy with the result, and now I'm really looking forward to the race.
"We've strong pace, and no matter the conditions we should be in good shape.
"It's difficult to foresee how the weather will behave tomorrow [Sunday], although the forecast has it a little friendlier than today [Saturday].
"We're expecting dry conditions, but it doesn't really matter. We are in decent shape.
"If it's mixed conditions then it could be an interesting race, and there are a lot of things that could happen on every lap."
A mix of rain and sun is forecast on Sunday, which could play into Hamilton's hands given how he has gone backwards in the dry of late due to the excessive tyre wear on his Mercedes.
It could also favour Valtteri Bottas as the Finnish rookie was the surprise qualifying package, claiming third in a Williams whose best grid slot prior to today had been 14th.
Bottas was naturally jubilant as he said: "This means a lot.
"The first six races have been so difficult, so this is a nice boost to the team. We got everything right today [Saturday].
"For tomorrow [Sunday] we definitely need more rain. In the dry the car does not belong in P3 at the moment, so rain would help."
Rosberg will start fourth ahead of Ferrari's Fernando Alonso, whose team-mate Felipe Massa crashed again after twice doing so in Monaco, with the Brazilian down in 16th.
Massa brought out the red flags with just two minutes of the second session remaining, which surprisingly was the only major incident.
With McLaren duo Sergio Perez and Jenson Button 12th and 14th, it is the first time since 2003 the team - winners here for the last three years - have failed to get a car into the top 10.
An angry Paul Di Resta will start 17th for the second successive race, and as in Monaco he has blamed Force India.
Di Resta said: "We spent far too much time trying to fix a problem when the conditions were good when the car could have run.
"It's the fault of the team again. It's just not good enough."
The stewards later handed penalties of a drop of two-grid positions to Lotus' Kimi Raikkonen and Daniel Ricciardo of Toro Rosso for not starting from the fast lane when the second session of qualifying restarted in the wake of Massa's accident.
The duo will now start 11th and 12th respectively, with Sauber's Nico Hulkenberg and Sergio Perez of McLaren moving up to ninth and 10th.
By a bizarre quirk of the FIA rules, despite receiving two-place penalties, it later transpired Raikkonen and Ricciardo only drop one position apiece.
With Raikkonen's penalty applied first, he initially falls from ninth to 11th, so actually promoting Ricciardo from 10th to ninth.
Applying the Australian's penalty next, he then drops from ninth to 11th, pushing Raikkonen up one to 10th.
So the new grid sees Hulkenberg ninth, Raikkonen 10th, Ricciardo 11th, with Perez staying put in 12th.