St. Bonaventure (12-8, 2-4 Atlantic 10) led 81-80 after Charlon Kloof sank two free throws. Colter rebounded a missed free throw with 4 seconds to play and drained the game-winner at the other end.
Marquise Simmons broke a 23-23 tie with a layup to put St. Bonaventure ahead and the Bonnies led 44-38 at halftime.
Colter's 3 pointer put Duquesne up 55-53 at 15:31 in the second half, and the lead traded hands four times until Matthew Wright hit a 3-pointer with 47 seconds left, giving the Bonnies a 79-78 edge. Soko hit a pair of free throws to make it 80-79 with 21 seconds left, then he fouled Kloof.
Kloof finished with 23 and Wright 22.
Maryland point guard Melo Trimble, considered a lock to leave the program before struggling in the second half last season, has withdrawn from the NBA draft and will return for his junior season.
Louisville's Chinanu Onuaku, who recently underwent a medical procedure to correct a heart rhythm issue detected during the combine, will keep his name in the NBA draft pool.
Andrew White III will return to the Nebraska men's basketball team next season after removing his name from the NBA draft.