Mike Talley finished with 12 points for the sixth-seeded Eagles (21-13), who will go up against second-seeded Toledo on Friday in the semifinal round.
Joshua Freelove scored 26 points, while Will Regan registered a double-double with 16 and 10 boards for the third-seeded Bulls (19-10). Jarod Oldham added 10 points, while Javon McCrea filled his stat line with 13 rebounds, seven points, five assists and four blocked shots, but converted only 2-of-13 from the floor.
Buffalo shot just 31.3 percent from the field in the opening half, yet managed to make good on 8-of-16 from 3-point range, as it led 32-29 at intermission. EMU made 38.7 percent of its field goal attempts in the period.
The Eagles connected on 40.7 percent of their shots from the floor in the second period and went 14-of-19 at the free-throw line. With 7:09 remaining in regulation, the game was tied at 55-55 but the Eagles went on a 7-0 run to create some space and then held on for the victory.
EMU's bench outscored the Bulls' reserves, 19-2.