The Impact (14-12-7) erased a 1-0 deficit in the 64th when Marco Di Vaio scored his MLS-leading 20th goal of the season with a curling shot off a feed from Davy Arnaud.
Ouimette then notched the game-winner on a header following a Justin Mapp free kick.
At 49 points, Montreal -- which climbed into third place in the Eastern Conference -- got closer to wrapping up a post-season berth.
Fabinho scored in the 29th minute for the sixth-place Union (12-11-10), whose playoff fate remains undecided with a one game to go against Sporting Kansas City.
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