Brian Oliver and Fuquan Edwin each had 10 points for the eighth-seeded Pirates (16-16), who have two of their last three games and will face top-seeded Villanova on Thursday.
Khyle Marshall scored 22 points and Kameron Woods cleared 12 rebounds for the ninth-seeded Bulldogs (14-17).
Seton Hall shot only 34.5 percent from the field in the opening frame but it still led 23-22 at the break. Butler made just 35.7 percent of its field goal attempts, including 1-of-11 from 3-point range.
The Pirates went on a 22-11 run over the first 10:15 of the second half to make it a 13-point game. The Bulldogs mounted a comeback, going on a 17-6 run over the next nine minutes to get within one, 51-50, with 46 seconds left. Neither team would score down the stretch however, and Alex Barlow missed the potential game-winning 3-pointer at the buzzer for Butler.
Despite Seton Hall only shooting 5-of-20 from beyond the arc, Butler was even worse by making just 2-of-18 from 3-point range.