Howard, who entered the day as the nation’s top scorer at more than 25 points a game, added eight rebounds before fouling out to lead the Golden Eagles (10-3, 1-1 Big East).
Cole Swider and Justin Moore each had 14 points for Villanova (10-2, 1-1), which had won its last six games.
The difference came at the foul line — Marquette made 26 of 30, Villanova 3 of 5. The Golden Eagles also had seven blocks — four by Theo John.
Marquette shot more than 55% from the field in the first half and was 13-for-13 from the line before the break. Marquette led by as many as 20 before holding a 46-30 advantage at halftime.
Howard scored 12 points in the first seven minutes and finished the first half with 17. Howard and Koby McEwen combined for 30 of the Marquette’s 46 first-half points. McEwen finished with 22.
Swider kept the Wildcats respectable early. The sophomore forward hit all four of his 3s in the first half and had12 points at intermission.
After losing to Creighton 92-75 in its conference opener, the Golden Eagles picked up a big victory at home and have now won six of their last seven games.
Villanova, which has won two of the last four national championships, now must quickly pick up the pieces after getting dominated on the road.
Villanova: Plays at Creighton on Tuesday.
Marquette: Hosts Providence on Tuesday.