New York (16-9-6) will secure the Eastern Conference regular-season title with a win or tie in either of its two remaining matches. The Red Bulls are three points ahead of Los Angeles and FC Dallas in the race for the overall lead.
Ambroise Oyongo was shown a red card for a hand ball on what otherwise would certainly have been a goal by Bradley Wright-Phillip in the 15th minute, leaving Montreal (12-13-6) a man down.
Kljestan put away the ensuing penalty kick.
Wright-Phillips slipped behind the defense on a breakaway, pulling goalkeeper Evan Bush out to the top of the box, but couldn't convert either of two shots. The second, however, ricocheted back to Sam, who chipped over a scrambling Bush to make it 2-0 going into the half.
Didier Drogba converted a penalty kick in the 67th for Montreal.