The Eagles (10-4) won their sixth game in a row and advanced to play third-seeded Delaware in the semifinals.
It's Southern's first appearance in the semis since 2002.
"Every week, people don't expect us to win," Eagles kicker Adrian Mora said. "They treat us like the underdogs. I like it, the team likes. Every game, we come out with a chip on our shoulder. It doesn't matter who's put in front of us now."
Mora had field goals of 33, 21 and 37 yards -- the last with just under 11 minutes to go to give Georgia Southern a 23-13 advantage.
The Terriers, co-champions in the Southern Conference after winning just three games a year ago, outgained Georgia Southern 343-246 in total yardage. They had a 195-55 advantage in the second half.
But Wofford fumbled six times, losing two, and had several untimely penalties.
Georgia Southern's defense forced five first-half fumbles, recovering two.
Defensive end John Douglas, of Augusta, scored on a 20-yard return of a Mitch Allen fumble to make it 14-0.
Only 15 seconds earlier, wide receiver Tray Butler and quarterback Jaybo Shaw connected on a 25-yard pass play for the opening score.
Christian Reed got Wofford (10-3) on the scoreboard with a 21-yard field goal with just over a minute left in the first half.
But Southern matched the field goal when Mora nailed a 21-yarder after an 8-play, 56-yard drive.
"Obviously, it was a big, big field goal," Eagles coach Jeff Monken said.
The Terriers inched closer when Allen and Brenton Bersin teamed on a 37-yard touchdown pass in the third quarter.
Reed added to field goal to bring Wofford closer.
In the final minutes, a controversial face-mask penalty on the Terriers allowed the Eagles to nearly run out the clock.