The Venezuelan was on fire in the first half, and the Crew held on despite late pressure from Philadelphia.
Bernardo Anor opened the scoring in the 24th minute, losing his marker and nodding in Federico Higuain's corner kick.
Anor's second came in first-half stoppage time, and it was a fantastic strike. Philadelphia's Cristian Maidana coughed up the ball in midfield, and Anor seized it, charged forward and unleashed a long-range strike that beat Zach MacMath.
Philadelphia fought back in the second half, and made it 2-1 in the 62nd minute. Ray Gaddis' cross was poorly headed away by Giancarlo Gonzalez and fell to Sebastien Le Toux, who played the ball back across the goal to waiting substitute Leo Fernandes.
Jack McInerney went close twice, his most dangerous chance coming with a sliding touch at the far post on a Brian Carroll cross, and Fernandes nearly equalled Anor's tally when he was denied by Steve Clark, but the Union were unable to force the equalizer.
Philadelphia falls to 1-1-1 on the season, with Columbus remaining 2-0-0.