The Hawks (10-21) won despite scoring six points over the final 11:19 of regulation, but sank 18 of 20 free throws in overtime and their only two field-goal attempts. Saint Joseph's will face Duquesne in the quarterfinal round Friday in Atlantic City.
The No. 12 and lowest-seeded Hawks never trailed, shot 52 percent from the field (23 of 44) and led 31-20 at halftime. Carl Jones scored 12 points and C.J. Aiken added 11. They finished 21 for 24 from the free-throw line.
Playing on their home court, the fifth-seeded Colonials (17-14) trailed 43-29 with 11:19 remaining, but closed the second half on a 20-6 run to send the game to overtime.
Tony Taylor's two free throws with 59.9 seconds left tied the score at 49 but his game-winning attempt in the closing seconds of regulation missed as did an attempted tip-in by Jabari Edwards. The Colonials went 3:33 into overtime before Taylor, who scored 19 of his 22 points after halftime, made a 3-pointer.
Jones, the Hawks' leading scorer on the season, and Ronald Roberts began the game on the bench for disciplinary reasons after being late to a team function.
The Colonials, who finished the regular season tied for fourth place, shot 35.7 percent in the game (20 of 56).