Prince Okoroh added 13 points for the Bison (8-24), who will face top-seeded N.C. Central in the quarterfinals on Wednesday after scoring the last seven points in this one.
Lamont Middleton scored a game-high 19 points and added eight rebounds for the Aggies (9-23), who lost seven of their last eight.
Middleton completed a 3-point play with 2:33 left in the game to put the Aggies ahead 47-46 but Howard responded with a 3-pointer from James Daniel to take the lead back for good, sparking a 7-0 run over the last 2 1/2 minutes.
There were four ties and five lead changes and neither team led by more than four points throughout the first 20 minutes.
2014: The Year in Music [PHOTOS]