The Bears (20-7, 12-2 Atlantic Sun Conference) used a 13-2 run to turn a six-point deficit with 13:26 remaining into a five-point lead, then held on to deny the Owls (3-23, 0-14) their first league victory.
Kennesaw State got to 53-52 on a Spencer Dixon 3-pointer with 5:14 left, but could not pull ahead.
There were four lead changes in the first half, with Mercer leading 27-24 at the break.
The Bears outshot the Owls 55.8 percent (24 of 43) to 32.1 percent (18 of 56) to sweep the season series, having won 81-51 on Jan. 13.
Bud Thomas added 14 points, Monty Brown 12 and Langston Hall 11 for Mercer.
Dixon’s 19 points paced Kennesaw State, which has lost 14 straight.