The Gamecocks (2-1) scored on three straight possessions in the second half to turn an uncomfortably close game at half into a rare blowout.
While Giles averaged 10.3 yards a carry and got his first career touchdown, fellow freshman Kenny Miles looked just as impressive, running for 56 yards on five carries in one first quarter series before sitting out the rest of the game with a shoulder injury.
Florida Atlantic quarterback Rusty Smith was 21-for-31 for 198 yards.
Gamecocks coach Steve Spurrier is 37-0 in his career against teams not currently in the Bowl Championship Series. South Carolina has just five days to get ready for No. 5 Mississippi.
One thing Spurrier will likely address is kickoff coverage. The Gamecocks allowed an average of 26 yards on each return, a week after allowing 36 yards on kickoffs.
The Owls (0-2) trailed just 17-16 at halftime, but turned over the ball twice on their first three drives after halftime. Stephon Gilmore picked off Rusty Smith's pass, and Eric Norwood sacked Smith to force a fumble.
The Gamecocks took advantage of the short field both times.
Gilmore later recovered a fumble as South Carolina forced three turnovers in the second half and stopped Florida Atlantic on a fourth down at the Gamecocks' 5.
The game got out of hand that.
With more than 3 minutes to go, Spurrier put in his son Scotty. On his second play, the senior caught a 13-yard pass for his first career reception.
South Carolina quarterback Stephen Garcia was 20-for-27 for 222 yards, throwing for one touchdown and running for another.
The discovery of a running game meant the sophomore didn't have to match the 53 passes and 313 yards he had in a loss to No. 23 Georgia last week.
Maddox gained just 23 yards on 10 carries and had just two catches for 8 yards, but managed three touchdowns.
South Carolina took a 17-3 lead on Garcia's 15-yard run with 8:53 left in the first half, but the Owls scored twice before halftime.
Smith's 3-yard touchdown pass to a wide open Jamari Grant with 16 seconds left in the second quarter made it 17-16 just before halftime and raised hope Florida Atlantic might beat a BCS team for just the second time in the program's nine-year history.
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