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.