With the loss, Montreal (12-12-10, 46 points) was eliminated from a spot in the postseason and finished 10th in the Eastern Conference.
Orlando City (13-9-12, 51 points) snapped a four-game winless run to close out the campaign. The Lions landed the sixth spot in the East.
Jhegson Mendez gave Orlando a 1-0 lead in the 55th minute when Montreal defender Rudy Camacho's clearing attempt landed at Mendez's feet for a long-distance strike.
Romell Quioto scored to tie it in the 59th minute but was flagged for offside and the call stood after video review. Montreal coach Wilfried Nancy was shown a yellow card after trying to argue the call.
Camacho was shown a direct red card after a tackle on Daryl Dike in the 79th minute, leaving Montreal to play the rest of the match with 10 men.
Daryl Dike drove to the box and won a battle against Zachary Brault-Guillard to make it 2-0 in the 88th minute.
Both sides exchanged opportunities in the first half.
In the 10th minute, with the Lions pressing, Benji Michel fired from the top left corner of the box but his shot went over the crossbar. Two minutes later, Montreal goalkeeper Sebastian Breza dove to the right to push away Mauricio Pereyra's attempt on a free kick.
Montreal pressured a few minutes later, maintaining possession in the box before Brault-Guillard took aim from the right side but Orlando goalkeeper Pedro Gallese came up with the save.
Gallese delivered again in the 21st minute. Montreal found several open seams before an uncovered Joaquin Torres fired from the box but Gallese came out to deny the Argentine with a quick leg save.
In the 37th minute, Orlando central defender Robin Jansson missed the opening tally by inches when his free kick grazed the right post and stayed out.
Sunusi Ibrahim scored for Montreal in the 39th minute but the goal was waved off with Sunusi Ibrahim flagged for offside.
Djordje Mihailovic came close to breaking the scoreless draw early in the second half. After his shot was blocked by Jansson, Mihailovic got his foot on the rebound but it hit the post in the 49th minute.