Travis Smith went 4-of-4 shooting from both the foul line and beyond the arc to finish with 16 points for Mercer (23-10).
Mercer will play in the A-Sun Finals on Saturday afternoon.
Tied 57-all, the Bears used a 6-0 run to separate from the Spartans. Thomas hit a jumper and Daniel Coursey converted two baskets during the stretch to put Mercer ahead 63-57 with 1:39 remaining.
Adrian Rodgers made two free throws with 1:25 left to cut SC Upstate's deficit to 63-59, but Mercer made seven free throws in the final 45 seconds to seal the victory.
Torrey Craig scored 20 for the Spartans (16-17).
Hall became the 35th member of Mercer's 1,000-point club with 1,010.