Glenn Bryant added 12 points and J.R. Sims chipped in 11 for seventh-seed Eastern Michigan (20-13), which takes on third-seed Buffalo in the next round.
Jordan Threloff and Aaric Armstead each scored nine points and combined for 19 rebounds for seventh-seed Northern Illinois (15-17).
It was Northern Illinois that led 35-24 at halftime. The Huskies shot 47.8 percent from the field on the opening frame, while the Eagles managed only five field goals.
The tables turned in the second half when Northern Illinois had all of three field goals. Eastern Michigan only hit on 30.8 percent from the floor, but also sank 12-of-15 at the free-throw line to rally for the win.
Eastern Michigan doubled up Northern Illinois in points off of turnovers (16-8).