Toronto FC won 3-2 on the night, but the aggregate was 3-3, thanks to a 1-0 victory in the first leg in Montreal last week.
Kenny Cooper also scored for Montreal, whose first-leg goal came from Jack McInerney.
The Impact will meet the winner of the Vancouver Whitecaps-FC Edmonton semifinal to determine who will represent Canada in the 2016-17 CONCACAF Champions League. The Impact advanced to the final this year, losing to Club America of Mexico.
Jozy Altidore, Benoit Cheyrou and Sebastian Giovinco scored for Toronto.