Kent State (18-8, 9-4 Mid-American) moved into a first-place tie with Bowling Green in the East Division of the MAC.
Chris Ortiz scored 13 for the Golden Flashes, while Khaliq Spencer had 10 points and 10 rebounds.
Kent State used a 25-6 run midway through the first half to open up a 32-21 lead and never trailed.
Ball State (7-17, 2-11) twice pulled within two early in the second half and a three-point play by Bo Calhoun, who scored 18 points, trimmed the deficit to four with 3:30 to play.
Manley answered with a 3 and, after Calhoun made 1 of 2 free throws, Gary Akbar hit a layup to make it 53-45 with 1:53 remaining.
Kent State made 5 of 7 free throws to seal it.