Zardes scored in the 44th and 62nd minutes as the Crew (9-11-7, 34 points) moved to two wins and a tie in the past three games.
Montreal (10-9-7, 37 points) lost for the first time in three games but spoiled the shutout bid of former Montreal goalkeeper Evan Bush when Romell Quioto scored in the second minute of second-half stoppage time.
As it stood, the second goal by Zardes, his seventh of the season and third in the past two games, assured the Crew would improve to 3-1-2 in the past six games as they keep their Eastern Conference playoff hopes alive.
Zardes' first goal was a rarity for the Crew. It marked the first time in 14 games back to July 17 vs. New York City FC that Columbus had a halftime lead. The Crew is now 5-0-0, all at home, when up at the half and 7-1-1 when scoring first.
Montreal hosts New England on Wednesday.
The same night the Crew carries the league banner when they host Mexico's Cruz Azul for the Campeones Cup, the annual matchup of the reigning MLS and Liga MX champions.
After that the Crew is at Philadelphia on Oct. 3.