The Golden Eagles (11-12, 3-8 Big East) led by as many as 13 points in the second half but Seton Hall (15-8, 5-6) came back with a 16-4 run, making it a one point game with 1:23 remaining.
Johnson missed a jumper and then a free throw on a one-and-one. The Pirates took possession with 19 seconds left but missed both shot attempts, and Marquette's Duane Wilson converted two free throws for the final margin.
Sterling Gibbs led the Pirates with 16 points.
Marquette shot 3 of 7 and had three turnovers in the final five minutes. The Golden Eagles were missing leading scorer Matt Carlino after he suffered a concussion in Wednesday's game against Villanova.