Penn managed just four field goals in the first 13 minutes of the second half. While Zach Rosen led a spirited comeback that brought his team to within one possession, 53-50, on his three-point basket with 23.7 seconds to play, Harvard was able to close it out.
Corbin Miller sank one of two free throws with 17.4 seconds left, and after Tyler Bernardini saw a three-point try rim out, Kyle Casey hit two free throws with 1.6 seconds to play.
Rosen, who suffered through a 2-of-9 first half, finished with 16 points and Miles Cartwright chipped in with 12. But Bernardini, the Quakers' No. 2 scorer with a 14.9-point average, was held in check and went the entire game without a basket and two points.
The Crimson broke the game open with a 14-4 run midway through the second half. Miller, who scored 17 points, came off the bench to deliver three-point baskets at the start and the end of the rally, the latter one giving Harvard a 44-34 lead with 7 minutes, 22 seconds to play.
Miller then answered a three-ball by Rosen with a long two from just inside the line. Penn finally got its offense in gear but the Crimson always seemed to have an answer. Casey, who also had 17 for Harvard, muscled up an inside basket to keep his team's lead at eight, and Oliver McNally answered Rosen's pair of free throws with two of his own, giving the visitors a 51-43 lead at 2:33 to play.
The Harvard spurt came after the Quakers rallied from an early second-half deficit with seven straight points. Penn missed its first nine field-goal attempts in the second half but two free throws by Bernardini, a layup by Rosen and Cartwright's three-point bucket moved Penn into a tie, 30-30, with 12:30 to play.
But the visitors tightened up on defense, holding Penn to just one basket in a 41/2-minute stretch while extending their lead into double digits.