Montreal was trailing 1-0 in the 78th when right back Zarek Valentin put a volley past Columbus goalie Andy Gruenebaum to it up, collecting his first MLS goal.
The Impact (6-11-3) then forged ahead with only a minute left when Justin Mapp was knocked over in the box by Crew midfielder Chris Birchall, leaving Bernier in prime position to score with a spot kick.
Milovan Mirosevic scored in the second half for Columbus (6-6-4).
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