The New York Police Department released few details about the arrest, saying only that the incident occurred Aug. 12.
Rhymes was arraigned on a charge of third-degree assault and was released on his own recognizance, said Barbara Thompson, a spokeswoman for the Manhattan district attorney's office. He is due back in court Oct. 24.
A lawyer for Rhymes, Scott Leemon, said the charge should have merited only a desk appearance ticket.
"This is payback by the NYPD," he said.
Police have wanted to interview Rhymes since the February shooting death of one of his bodyguards, Israel Ramirez.
Ramirez, 29, was killed outside a Brooklyn studio where Rhymes was recording a music video.
The performer and another bodyguard were sued the following month by a fan who says the two men beat him after he asked for the rapper's autograph.
Police arrested Rhymes Saturday evening after he performed at the AmsterJam Music Festival on Randall's Island. The New York Post said police believe Rhymes beat a man who spat on his car near Gramercy Park.