The shutout, just Columbus‘ third of the season, prevented United (6-4-4) from leaping above the New England Revolution into first place in the Eastern Conference.
Columbus (4-5-6) finished the season series against United with a win and two draws. The Crew won just once in its last 12 matches overall.
Clark saved the penalty simply by remaining upright.
Referee Hilario Grajeda awarded the kick after he ruled that Columbus defender Bernardo Anor handled the ball inside the penalty area.
Columbus earned the draw despite missing injured leading scorer Federico Higuain (hamstring) and Costa Rican World Cup call-ups Waylon Francis and Giancarlo Gonzalez.
The Crew were also without forward Alvaro Rey, who was acquired Friday from Toronto FC for Dominic Oduro.
United, which was without suspended midfielder Perry Kitchen, lost striker Eddie Johnson in the 58th minute to an apparent injury to his right leg.
Columbus created more of the second-half chances.
In the 55th minute, United goalkeeper Bill Hamid dove left to block Anor’s firm, low strike before Ethan Finlay fired his rebound effort well high.
Later, D.C. defender Bobby Boswell deflected Ben Speas’ shot from the right just inches outside the left post.
United almost got a break when Columbus defender Tony Tchani nearly deflected a cross into his own goal.
But on the other end, Hamid pushed away Adam Bedell’s strike in the 83rd minute after Finlay found Bedell from the right side.
Clark appeared to take down D.C.’s Steve Birnbaum inside the penalty area in the 89th minute, but Grajeda didn’t rule a foul.