Tyler Bernardini scored 15 points and led four Quakers in double figures. Jack Eggleston scored 14 points, and Brennan Votel and Harrison Gaines each had 12 for Penn (4-10).
Penn led 60-59 with 7:37 left in the game before Govens hit an 18-foot jumper that started a decisive 14-2 run for the Hawks. A layup by Garrett Williamson with 3:29 left capped the outburst that gave Saint Joseph's a 73-62 advantage.
The Quakers led by as many as 16 points in the first half, but lost their fourth straight Big 5 game.
Penn hit 10 of its first 17 shots on the way to a 24-8 lead with 10:30 left in the first half. But the Hawks, who missed nine of their first 12 field goals, scored 21 of the next 24 points to take a 29-27 lead with 4:24 left in the opening half.
The Hawks led 37-34 at the break. Penn fell to 0-10 this season when trailing at the half.
Nivins, who had his 11th double-double of the season, opened the second half with a dunk and 6-foot jumper, and the Hawks scored 13 of the first 20 points in the half to lead 50-41 with 15:16 remaining.
Penn, helped by consecutive 3-pointers by Kevin Egee, scored 17 of the next 26 to take a one-point lead with 7:37 left, but failed to hang on.
