The Catamounts (8-7) were up 65-56 after a 3-pointer from Ernie Duncan with 4:04 to play. Despite missing 3 of 4 free throws, Harvard (6-8) cut the margin to three on Corbin Miller's trey with 1:41 remaining.
But the Crimson missed their last two shots, including Corey Johnson's 3-point attempt with two seconds left.
Ernie Duncan added 14 points and Trae Bell-Haynes had 10 with five steals and four assists for Vermont, which shot only 42 percent
Agunwa Okolie led Harvard with 16 points, Miller had 15 on five 3s and Johnson 14. Zena Edosomwan had 10 rebounds, eight points and four blocks. The Crimson, down 32-27 at the half, shot 50 percent in the second half with four 3s.