Senior Superintendent Wayne Minnaar said the raid followed numerous complaints from the high court and business owners in the city.
"The vagrants were making it impossible for anyone to walk on the pavement on Prichard, Kruis and Von Brandis streets. Some pedestrians had been attacked and robbed by some of the vagrants."
Minnaar said all women and children were being released on a warning. Men were being released after paying the R300 admission of guilt fine.
"Those who do not have the money to pay the fine would have to appear in the Johannesburg Magistrate’s Court on Monday."
Mdecins Sans Frontires (Doctors Without Borders) in South Africa said a total of 344 Zimbabweans were arrested outside the Central Methodist Church and the South Gauteng High Court.
"Nursing staff from the MSF clinic, operating at the church – where more than two thousand Zimbabwean men, women and children seek refuge – witnessed police manhandling some of the homeless Zimbabweans.
"When police officers rounded the Zimbabweans up they were pushed to ground and some were threatened with electric stun guns," said MSF spokesperson Borrie La Grange in a statement.
Minnaar said those arrested were not mistreated: "We can’t assault innocent people, that’s not true."
La Grange said most people were still being detained late on Saturday morning because not paying the R300 fine.
"These people have not paid the fine, not that they don’t want to, [but] because they do not have it [the money]."