The Highlanders (2-2) held a one-point lead, but closed the first half with a 13-0 surge sparked by 3-pointers from Winfield Willis and Emmanuel Tselentakis to take a 46-32 lead into the break. They shot 52.8 percent from the field led by as much as 21 in the second half.
New Hampshire (2-1) cut the deficit to eight on a Chris Pelcher free throw, but with just 46 seconds remaining.
Damon Lynn finished with 13 points for NJIT and sank a trio of 3-pointers.
The Wildcats were just 23 of 60 on field goal attempts and shot 25.8 percent from beyond the arc to NJIT's 64.3 percentage. They were paced by Pelcher, who scored 20 points and hauled in 15 rebounds, both game-highs.