Charleston (3-1, 1-1) took a 3-0 lead with 39 seconds left in the first quarter on a 22-yard field goal by Puma Nuredini.
Shepherd (3-1, 2-0) cut the lead to 10-7 when senior cornerback Keon Robinson picked off a pass and raced 48 yards for a score with 31 seconds left in the half. Redshirt freshman Ryan Earls added the extra point.
Shepherd took a 14-10 lead when junior running back Jihad Rasheed scored on a 6-yard run with 10:17 left in the third quarter.
The Rams added a safety when Charleston quarterback John Knox was called for intentional grounding in the end zone after being pressured by junior defensive end Howard Jones with 12:21 left in the fourth quarter.
Junior running back Mike Haynes rushed 24 times for a game-high 104 yards to lead the Rams. Jordan Roberts rushed 12 times for 20 yards for the Golden Eagles.
Senior quarterback Bobby Cooper completed 11 of 27 passes for 88 yards. Maurice Leak connected on 13 of 33 passes for 144 yards for Charleston.
Shepherd had 303 yards of total offense, while holding Charleston to 191.