Jakob Gollon added 18 points and Bud Thomas scored 12 for the Bears who finished the game on a 16-4 run after Jacksonville had closed to within 53-51 with 5:48 left.
Mercer (23-8, 14-4) will get the No. 2 seed in the A-Sun tournament due to the tiebreaker favoring co-champion, Florida Gulf Coast.
With the No. 7 seed, Jacksonville (12-17, 8-10) will return to Mercer's Hawkins Arena on Tuesday for an immediate rematch in the conference quarterfinals.
After shooting no free throws for the first 30 minutes, the Bears finished the game 14 of 22 from the line.
Jarvis Haywood had 13 points for the Dolphins who nearly erased a 44-26 deficit, only to fall back in the final minutes.