In a statement, the South African Human Rights Commission said it "will institute legal proceedings against Mr. Eben Etzebeth in the Equality Court" on Friday.
Etzebeth, 27, allegedly insulted, assaulted and pointed a gun at a 42-year-old homeless man in Langebaan, a seaside resort about 120 kilometres north of Cape Town in August.
He was named in South Africa's squad for the World Cup in Japan just a day after the allegations surfaced on social media.
The 78-cap lock was interviewed by Human Rights Commission officials before flying out with the South African squad. He denied the allegations.

The commission said it would meet the complainant on Thursday to take further instructions.
"We will definitely ask for monetary compensation, we will ask for a public apology, we will ask for criminal prosecution of Mr Etzebeth, we will ask for community service and other forms of relief," Buang Jones, acting head of legal serves at SAHRC told AFP.
The commission will also hold a public meeting on Thursday in the town.
"The community are demanding justice, so we are going to give them a platform to ventilate around this matter," said Jones.
He also said the commission will approach the country's police service to ask it to look into claims of bias against a police officer who initially investigated the matter.
South Africa's rugby body, SA Rugby has vowed to cooperate fully with investigations and promised to "take appropriate action once the legal investigation and process have concluded".

Source: East Coast Radio