Aaron Miller passed only twice during the game but ran for 83 yards and a score for the Bulldogs (3-6, 1-3 Southern). Isaiah Smith ran for 53 yards and two touchdowns as The Citadel amassed 493 yards rushing.
Smith's 21-yard touchdown run with 43 seconds left in the first half put the Bulldogs up 28-10 at the break.
In the third quarter, Mercer's Jagger Lieb kicked his second field goal and Avery Ward caught a John Russ pass for a 65-yard scoring play. Alex Lakes ran for another touchdown late in the fourth but the 2-point conversion failed.
Russ threw for 178 yards and a touchdown and ran for 96 yards and another score for the Bears (5-5, 1-5).