Court documents report Harris, 30, became angry with his boyfriend Dimitri Geier, at Su Hung restaurant in Menlo Park in August.
County Prosecutor Al Serrato said Monday Harris got angry when Geier attempted to put soy sauce on Harris' rice.
"Basically, they're having dinner together and they get into a verbal dispute and it gets violent from there," Serrato said.
Harris then accused Geier of stealing his underwear, Serrato said, and tried to pull down Geier's pants, before pinning Geier against a glass window and hitting him several times in the face and head.
San Francisco Chronicle said Geier suffered multiple facial fractures and underwent surgery.
Prosecutors said Harris was charged with felony domestic abuse with great bodily injury and assault with great bodily injury.
He pleaded not guilty and is scheduled to go to trial in April, prosecutors said.
Harris played for the 49ers for five years before signing with the Raiders as a free agent. He was released in 2008.