Comer scored 21 points in the win, which gave the second-seeded Eagles (24-10) the Atlantic Sun Tournament crown and the first trip to the NCAA tourney in school history.
Sherwood Brown had 16 points and 11 rebounds for the Eagles, and was 4-of-5 from 3-point range. Chase Fieler added 15 points.
Travis Smith led Mercer (23-11) with 16 points and Jakob Gollon and Bud Thomas scored 14 apiece.
The game was played on Mercer's home court where the Bears went 15-0 in the regular season.