Hamilton, who had set the pace in the opening Friday practice from Valtteri Bottas, lost control of his W10 on exit of Turn 9 when running the medium tyre early on in FP2.
He slid off into the outside wall, making contact with his right-rear tyre - and while he then successfully brought his W10 back to the pits despite the damage, Mercedes was forced to change the rear suspension and he did not return for the rest of the session.
Mercedes, which has introduced an upgraded power unit in Canada, was dominant in FP1, but its rival Ferrari team locked out the top two spots in the second session.
Valtteri Bottas, who in Hamilton's absence finished FP2 0.134s down on the pace-setting Ferrari of Charles Leclerc, said his Mercedes "feels strong" but stills needs work in terms of balance.
"The car seemed strong on both long and short runs, but Ferrari was very quick on the straights, so I expect it to be a very close fight tomorrow."