Bishop Paul Veryn of the Central Methodist Church which was attacked told SABC radio: "We consider that the situation is getting so serious that the police can no longer control it."
As night fell, immigrants were streaming into one police station near downtown Johannesburg carrying whatever belongings they could, reports Caroline Hawley.
Many now fear for their lives, she reports. One Zimbabwean woman told the BBC she would flee back home rather than risk losing her two children to the mobs.
Foreigners have been trying to flee the violence
The trouble began a week ago in the sprawling township of Alexandra. Immigrants from neighbouring African countries were set upon by men with guns and iron bars chanting "kick the foreigners out".
Terrified Zimbabweans, Mozambicans and Malawians fled to the safety of the local police station and to another township, Diepsloot.
They were then attacked there as well - shacks were burnt down and shops looted. The violence has since spread to other areas.
Since the end of apartheid, millions of African immigrants have poured into South Africa seeking jobs and sanctuary. But they have become scapegoats for many of the country's social problems - its high rate of unemployment, a shortage of housing and one of the worst levels of crime in the world.
Police have been trying to restore order in Diepsloot township
The South African Red Cross is now providing food and blankets to hundreds of frightened immigrants forced from their homes.
President Thabo Mbeki said he would set up a panel of experts to investigate the violence.
The leader of the governing African National Congress, Jacob Zuma, condemned the attacks.
"We cannot allow South Africa to be famous for xenophobia," he told a conference in Pretoria.
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