Howard, the country's leading scorer, entered the game averaging 27.4 points. He shot 8-of-20, including 5-of-11 from 3-point range, to go along with 5 rebounds and 2 assists for No. 18 Marquette, which had won three straight and six of seven prior to Wednesday's 72-71 loss.
Howard passed Syracuse's Lawrence Moten (1,405 points) for the scoring record in Big East play.
"Markus has had a historical career,'' Marquette coach Steve Wojciechowski said. "But I can tell you he's not in the locker room right now thinking at all about those records. When his career is over -- hopefully that's a long way down the road -- he'll be able to take in the history that he's created at Marquette and in the Big East Conference.''
The No. 15 Wildcats led by as many as 15 points in the first half and came out strong to open the second half. Villanova scored the first nine points after the break, five of which came from the free throw line, to lead 47-29 with 16:27 remaining. Marquette continued a pattern from the opening 20 minutes by missing its first six shots after the break.
The Golden Eagles slowly cut into the Villanova advantage. They narrowed the deficit to 65-60 with 3:58 remaining on Koby McEwen's 3-pointer from the left corner. The Wildcats tallied the next five, capped by Collin Gillespie's 3 with 2:03 left.
But Howard's 3 with 43 seconds left pulled the Golden Eagles within 71-68. After Saddiq Bey missed, Villanova intentionally fouled Howard. He missed the first and then failed to hit the rim while trying to miss the second, giving the ball to Villanova.
Jeremiah Robinson-Earl then made the second of two free throws with 4 seconds left before Howard drained a 3 at the buzzer.
The Golden Eagles have a rare weekend off before returning to action next Tuesday at home against Creighton. Marquette can gain some momentum for the postseason by playing three of the next four at home before finishing the regular season on the road at DePaul and St. John's.
The Associated Press contributed to this report.