For the last three years Hamilton has put his Mercedes at the front of the grid but on Sunday it will be his Ferrari championship rival Sebastian Vettel holding the edge while the Briton will start from fourth.
With their chief rivals bringing upgraded power units to Montreal, Mercedes were expected to be at a disadvantage as they tried to squeeze a seventh and final race out of their engines.
But on Saturday it was not the engine that let down Mercedes but rather their four-times world champion who admitted to having a rare bad day at the office while team mate Valtteri Bottas joined Vettel on the front row.
"In my heart I felt we had the pace to lock up front row," said Hamilton, who has six poles in Montreal to go along with his six victories. "I had the pace to be on the front row but just struggled in the session and wasn't able to pull it through.
"Usually the last sector is actually my strongest at this track but I was just struggling into turn 10. Constantly today I was struggling going into that corner... it was quite messy.
"That definitely was a good chunk of time there, just in that corner alone was pole position for sure."
"Can't get them all and I will try to recover from it tomorrow."
Mercedes knew coming into the Canadian Grand Prix that they were taking a gamble, saying on Wednesday that they would delay the introduction of a power unit upgrade until after this weekend’s race due to a “quality issue”.
Despite that, Mercedes performed well in all three practice sessions followed by a superb effort from Bottas in qualifying.
Still, an upgrade might have made all the difference on Saturday, suggested Mercedes team boss Toto Wolff.
"If we would have brought the engine upgrade would it have been an advantage?" asked Wolff. "It definitely would have made a difference today.
"Would it have been enough to qualify for pole or Lewis to qualify on the front row we don't know but again it is one of the things that probably would have changed the overall outcome.
"In so far as we can't miss out on the tiniest of upgrades and smallest of mistakes we will be penalised.
"This is going to make the difference between winning and losing the weekend."
(Editing by Clare Fallon)
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