It was the seventh straight victory for the Crimson (16-7, 8-1) over the Bears (9-14, 3-6), including 89-82 in two overtimes on Feb. 2.
Harvard exploited 14 first-half turnovers by Brown to gain control. The Crimson led 26-9 before the Bears rallied in the final 2:51 of the half to trail 29-18 at the break. Siyani Chambers, who finished with 14 points for Harvard, had four first-half steals.
Brown got to within six, 39-33, with 10:29 remaining, but a jumper by Christian Webster, a free throw by Steve Moundou-Missi and a dunk by Saunders gave Harvard an 11-point lead.
Neither team was effective behind the 3-point line. Harvard made 2 of 12 and Brown just 1 of 14.
Cedric Kuakumensah led the Bears with 11 points and Sean McGonagill added 10.