Kansas City (10-5-2) ended a three-match winless streak and moved past New York into second place in the Eastern Conference.
Patrice Bernier put Montreal in front in the 49th minute, but Bernier was called for a hand ball in the penalty area in the 55th minute to set up the successful kick from Kamara.
The game remained tied until Montreal's Davy Arnaud committed a foul in the box which led to Zusi's go-ahead penalty kick in the 75th minute.
Jacob Peterson added to the Kansas City lead 7 minutes later with a right-footed blast from outside the box.
Montreal (5-11-3) lost its third in a row.