Leading 39-36 with 18:49 left, the Great Danes (4-6) used a 20-7 run to pull away. Albany shot 57.1 percent (16-for-28) from the field in the second half while the Quakers were 34.8 percent (8-for-23).
Penn (0-6) which won't play again at home until Jan. 13 against Temple, is off to its worst start since beginning the 2000-01 season 0-8.
Mike Johnson added 15 points and seven assists for Albany.
Albany won 73-63 last year in the only other meeting between the two schools.
Mike Brey is looking at former Notre Dame players to fill two assistant jobs that have opened up with the departures of Martin Ingelsby and Anthony Solomon.
Purdue's 2016-17 prospects got a jolt Wednesday when forward Caleb Swanigan announced he will return for his sophomore season.
Clemson's Jaron Blossomgame says he is withdrawing from the NBA draft and returning to school for a final season.