Dante Cunningham stole in the in-bounds pass, was fouled and clinched the win with two free throws, sending the Villanova student section into a frenzy. Cunningham scored 14 points.
Villanova trailed most of the second half and appeared on the brink of losing for the second straight season to the Hawks (4-5). Ahmad Nivins, who scored 16 points, hit two free throws with 44 seconds left to give Saint Joseph's a 56-55 lead.
Playing only two nights after No. 6 Texas beat them 67-58 at Madison Square Garden, the Wildcats took over from there and won their second city series game of the season.
Darrin Govens had the Hawks hopeful of an upset with a hot hand from 3-point range, going 6-for-11 from outside the arc and leading them with 18 points.
While the rivalry between the schools has remained the most heated in the city among the six Division I teams, the games have become quite lopsided over the past few years. The average margin of victory entering Thursday was 17.1 points over the last seven games, including a 22-point win by Saint Joseph's last season.
This was one was vintage Big 5. All that was missing was the Palestra.
The long-time city rivals went on a 3-point spree that got the staid Pavilion crowd rocking. Tasheed Carr hit the first 3 for the Hawks, Dwayne Anderson answered with one, then Govens nailed his fifth 3 of the game for a 47-44 lead.
After a timeout and empty possessions for teams, Govens got the Hawks going again with yet another 3-pointer and a six-point lead with 5:44 left.
Reggie Redding hit two jumpers in about 90 seconds, one that pulled the Wildcats within one and the last one that finally put them ahead 53-52 with 2:55 left. That let the Villanova students start a "We can't hear you!" chant across the court to their suddenly subdued Saint Joe's counterparts.
The Wildcats did not attempt a free throw in the first and half and the Hawks went 2-for-2. Then it became a battle from the line down the stretch to decide this one.
Nivins made two from the line and the Wildcats took a 54-53 1:25 left only for Redding to make two at the 59-second mark for a 55-54 lead.
The Wildcats finished 13 of 15 from the line and needed them all to improve to 42-24 in the series.
Govens hit 35 percent of his 3s coming into the game and he connected on back-to-back shots to give the Hawks a 17-13 lead. His fourth 3 of the half stretched the lead to nine and Saint Joseph's took a 35-26 lead into halftime.