Afroman – best known for his 2001 hit Because I Got High – was seen hitting the woman, who was dancing on stage behind him at the Kress Live venue.
Biloxi Police said he was arrested for assault on Tuesday and later released on bail.
A spokesperson for the rapper said he would be issuing a formal apology.
An earlier statement issued on his behalf said it was “a completely involuntary reflex reaction to people infringing on his stage space,” according to Billboard.
“It was uncharacteristic behaviour that was initiated by outside uncontrolled forces,” the statement added.
Afroman, real name Joseph Foreman, was nominated for a Grammy in 2002 for best rap solo performance for Because I Got High.
A Biloxi Police Department statement said: “Mr Foreman was arrested for assault as a result of a citizen’s affidavit, booked in, and released after paying a $330 (£214) bond.”