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.
Colorado State graduate transfer John Gillon has chosen Syracuse, giving the Orange a potential starter at point guard entering the 2016-17 season.
DeSean Murray, who averaged 20.2 points as a sophomore at Presbyterian, will transfer to Auburn to play for coach Bruce Pearl.
Former Kentucky guard Ed Davender, the only Wildcat with at least 1,500 points and 400 assists, has died. He was 49.