Video showed Flowers making the obscene gesture to the student section in Orlando, Florida, after scoring a touchdown in the third quarter of the 49-42 loss.
"It was in no way my intention to do anything offensive in Friday night's tremendous game between two great teams and universities," Flowers said in the statement Saturday. "I apologize if anything I did was interpreted the wrong way. I have always tried my best to be a good representative of USF and a positive example to young people."
Flowers had a single-game school record 605 total yards in the loss, but his gesture drew scrutiny. It came a week after Oklahoma quarterback Baker Mayfield made a lewd gesture against Kansas and was disciplined for it.
USF coach Charlie Strong gave no indication that he intended to punish Flowers when the Bulls (9-2) play in their bowl game.
"I know who this young man is, I know his character and I don't believe he intended to do anything that would offend anyone," Strong said in a statement.