The home side started brightly and were on the front foot for most of the early stages, with Anibal Godoy coming close to breaking the deadlock when his long-range strike drifted just wide of the post.
Despite dominating possession for long spells, San Jose struggled to pick the right pass in the final third and wasted a great chance to take the lead when Marc Pelosi failed to find Quincy Amarikwa in space inside the box.
The Earthquakes were gifted the opening goal 10 minutes before the break when Montreal lost possession on the edge of the box, which allowed Chris Wondolowski to fire home after Amarikwa's path to goal had been blocked.
Montreal were dealt another blow early in the second half when Ambroise Oyongo was shown a straight red card for catching Wondolowski with a high foot.
San Jose piled the pressure on as they searched for a second goal, with Wondolowski sending a shot just wide of the post before Shea Salinas cleared the crossbar with a powerful strike.
Chances were difficult to come by in the closing stages, though, as San Jose missed the chance to climb up to fourth in the Western Conference.