The Tigers made just 17-50 field goals for 34 percent while the home team hit 43.6 percent from the field.
South Florida struggled with its foul shooting percentage, but got plenty of opportunities hitting 22-39 while Auburn was 8-14 at the foul line.
The Bulldogs dominated on the boards, holding a 40-28 rebounding advantage.
The Bulls from the Big East Conference, who improved their record to 6-5, were led by Jarrid Famous, who scored 15 points.
The game marked the season debut of junior guard Frankie Sullivan, who scored four points in nine minutes for the Tigers. The highlight of the game for Auburn was a four-point play by Sullivan with a second left in the first half.
Sullivan entered the game at the 8:52 mark with the Tigers trailing 17-15. The guard underwent ACL surgery over the summer and it was originally believed he would be out for the entire season.
USF had led by as much as 11 points at 17-6, but the Tigers put together a 13-0 run to take a 19-17 lead at the 6:59 mark. However, the Bulldogs regained the lead and built their margin to 28-20 before Sullivan's three-pointer from the wing followed by a foul shot on the play cut the halftime margin to 28-24.
South Florida built its first half lead with a 23-12 rebounding edge, but Auburn forced 11 turnovers and committed seven to keep the game close in the first half.
At the break the Tigers were shooting 28 percent from the field hitting just 7-25 field goals. The Bulls made 44 percent (11-25) in the first 20 minutes. The Tigers hit 3-8 threes and 7-9 free throws in the first half while USF made 3-10 treys and 3-8 free throws.
The Tigers stayed within striking range most of the second half, but could never make a run. USF built its lead to double figures with 8:58 left at 47-37 and pushed its lead out to 15 points in the final minutes.
Auburn coach Tony Barbee said the Tigers need to play with more toughness. "I thought we tried to defend, I thought we tried to play hard, but you can play hard and you can defend but you can also lack toughness and grittiness," he said.
"When you are an undersized and an under-manned team that is the aspect you have got to have," he said. "Two games in a row, we have lacked that.
"Where it shows up is on the backboard and the number of times you foul because you are always trying to play catch-up," he added. "Offensively, it is going to be a struggle this year."
Commenting on Sullivan's return, Barbee said, "It is going to be a work in progress with Frankie. When you are coming off that type of an injury you are not going to expect it right away. It usually takes a pretty significant time before you even get back to feeling close to normal so it is going to be a process."
Barbee added, "At least I know one thing about Frankie--half speed, 50 percent, whatever he is, he will give it everything he has got. He is going to be gritty and he is going to be tough. I hope that becomes contagious with some of the other guys."
The Tigers return to action for a Saturday home game vs. Presbyterian. Tipoff is set for 7 p.m. CST.