Neal Kitson made two saves to record his 12th shutout for St. John's.
Josh Carroll was issued a red card in the 23rd minute and Rutgers would be forced to play a man down for the remainder of the game.
"I thought our guys fought really hard," said head coach Bob Reasso. "We played with 10 men for 67 minutes ... and I thought our guys did pretty well. I think we've grown up a lot this year."
St. John's, the Red Division champion, has earned a No. 1 seed in the Big East Tournament and will receive a first-round bye. The Red Storm will host either Villanova or Providence in Saturday's quarterfinals.