Luke Greiner notched the game-winner late in the 2, in the Beanpot consolation contest on Monday evening at TD Garden.
Alex Killorn and Alex Fallstrom also tallied and Tommy O'Regan added two assists for the Crimson, who fell by a 3-1 count to Boston University in last week's semifinal.
Steve Michalek stopped 24-of-26 shots for the win as Harvard claimed third place for the second straight season.
Luke Eibler and Robbie Vrolyk scored for the Huskies, who dropped a 7-1 decision to Boston College in the other semi. Clay Witt played well in defeat, making 33 saves.
Northeastern finished fourth for the first time since 2008.
BC and BU will square off later Monday for the 60th annual Beanpot crown. The Terriers have won 29 times and the Eagles have claimed 16 titles.