In Durban, which seen some of the biggest protests, white tents housing mostly Malawians are being dismantled as authorities race to clear the transit camp.
Women in colourful sarongs sat on top of their belongings, waiting in line to board a bus home to Malawi.
One man, Nelson Mbewe, said he had gone to South Africa in search of employment to support his family in Malawi.
“But we’ve faced challenges – they’re saying we should go back home because we do not have the right documents,” he told the BBC.
“They say we are Makwerekwere” – a xenophobic slur used to refer to African migrants from other countries – Mbewe said.
“It’s their country, so what can we do? That’s why we have accepted that we just have to [unwillingly] go back home.”
Hassan Phiri, a Malawian who is still waiting to be processed, had a message for the protesters.
“All I want to say to South Africans is that we are all one. No matter what is happening, no matter what will happen, Africa must remain Africa.
“Africa can’t be Africa without South Africa… without Malawi, without anywhere,” he told the BBC, adding: “So whatever will happen, we must love each other and stick together as Africa.”
