Daniel Coursey added 12 points and blocked five shots for Mercer, which had 10 blocks as a team and held Lipscomb to just 33 percent (20 of 60) from the field.
Mercer (20-9, 12-4 Atlantic Sun Conference) jumped out to an early 12-7 lead behind seven points from Thomas. The Bears pushed that lead to 15, 29-14, behind a Justin Cecil 3-pointer with 5:27 left in the first half.
Lipscomb (12-16, 7-9) cut the deficit to 45-44 in the second half but Mercer used an 8-1 run to seal the win.
Mercer shot 42 percent (23 of 55) from the field and hit 12 of 16 free throws. Martin Smith led Lipscomb with 12 but the Bison struggled from the line, hitting 8 of 17 attempts.