Liberty tied with Lipscomb atop the conference but the Flames (25-6, 14-2) will go into the conference tournament as the second seed.
Lovell Cabbil had 15 points for the Flames.
Zach Cooks, who led the Highlanders in scoring heading into the matchup with 17 points per game, had only five points on 2-of-12 shooting.
The Flames swept the Highlanders in the season series. Liberty defeated NJIT 77-57 on Feb. 2.
NJIT will be the fifth seed in the conference tournament.