Alejandro Pozuelo's second-half penalty proved to be enough for Toronto at Saputo Stadium as the MLS season resumed.
The season was briefly postponed amid protests against racial injustice across the United States after the police shooting of Jacob Blake.
Pozuelo put away a spot-kick in the 50th minute for Toronto, which claimed its fifth win in eight MLS games and is unbeaten.
Toronto returned to the top of the Eastern Conference, sitting two points clear of Columbus Crew.
Thierry Henry's Montreal, meanwhile, sits fifth on the table.