Hamilton had completed just eight laps when he carried too much speed through the chicane at the Circuit Gilles Villeneuve, losing control of his Mercedes and hitting the wall.
The world champion sustained extensive damage to the right-rear of his Mercedes, somehow managing to limp back to the pits despite his tyre threatening to fall off.
"Sorry about that," said Hamilton following his uncharacteristic mistake.
Hamilton's Mercedes team confirmed that the floor of his car had been damaged in the accident, and following repairs, he did not re-emerge for the remaining hour.
The Englishman's weekend had begun in the best possible fashion after he blitzed the time charts in the opening running.
But, in Hamilton's absence, Charles Leclerc led a Ferrari fightback on Friday afternoon. The Monegasque finished on top, edging out his team-mate Sebastian Vettel by seven hundredths of a second. Valtteri Bottas was third, 0.134 sec adrift of Leclerc.
Mercedes have brought a new engine to Montreal, but Ferrari's speed in the afternoon, coupled with Hamilton's accident, suggests they might not have it all their own way.
Hamilton was not the only driver in the wars during the second running, with Max Verstappen also thudding the wall on the exit of the final bend.
The corner is nicknamed the Wall of Champions after Michael Schumacher, Damon Hill and Jacques Villeneuve all endured accidents there.
Verstappen's collision left a dent on the wall, but the Dutchman escaped without serious damage to his Red Bull.
Carlos Sainz finished an encouraging fourth for McLaren ahead of Haas driver Kevin Magnussen. Hamilton's time before his crash was good enough for sixth.
British teenager Lando Norris ended the day in 11th, some seven tenths adrift of Sainz in the sister McLaren.
Englishman George Russell had the better of Williams team-mate Robert Kubica again, finishing a third of a second ahead of the Pole, albeit 19th of the 20 runners.
