Jackson Donahue scored 17 points with four 3-pointers for his third straight double-figure scoring game and fourth this season. Antonio Woods had six assists and Penn never trailed.
The Quakers (6-7), who start the Ivy League season Jan. 9 against Princeton, made 12 of 32 3-pointers and outshot the Bearcats 48 percent to 24 percent.
Binghamton was scoreless for the final 7:33 of the first half while Penn scored 16, including 3s by Howard and Donahue, and led 37-14 at halftime.
The teams traded baskets in the second half until Howard hit another 3 amid a 14-0 run to lead 73-37 with 2:33 left. Penn began clearing its bench, with Collin McManus, Dylan Jones and Darnell Foreman seeing their first action of the season.
Willie Rodriquez led Binghamton (3-10) with nine points.