A Malawian traditional healer in Nquthu was nearly targeted by an anti-immigration march before a local chief intervened, even though the man is legally documented.
About 10,000 people marched through Johannesburg demanding undocumented foreign nationals leave the country, but the protest turned violent with looting and attacks on journalists.
Thousands of Malawians have been bussed from Durban to Musina as the eThekwini repatriation site shuts, but buses without travel certificates are being turned away at Beitbridge.
Foreign-owned shops across Protea Glen, Phiri, Mapetla, Sanoana, Dlamini and Tshiawelo in Soweto stayed closed on Tuesday, while residents and taxis carried on as normal.
Hundreds of Zimbabweans, mostly women and children, are sleeping outside at Epping Industria 1 in Cape Town, waiting for buses home after fleeing threats ahead of the 30 June deadline.
Police say they are ready for nationwide anti-illegal immigration protests and warn that anyone involved in violence, intimidation or looting will be arrested.
The United Nations has urged South Africa to protect human rights as anti-immigration protests begin, while Amnesty International accuses a leading group of pushing illegal citizen's arrests.
Thousands of foreign nationals have left South Africa over the past few weeks, as deportations rose 46% to 109,344 and Tuesday's 'leave or else' deadline set by anti-immigration groups arrives.
Foreign traders in Protea Glen, Soweto, were open for business on Monday despite pressure to shut down ahead of an unofficial June 30 deadline set by some community members.
The South African Post Office has exited business rescue, but many workers say they still fear for their jobs after years of uncertainty and thousands of retrenchments.
KwaZulu-Natal police have warned businesses that employ undocumented foreign nationals they should not expect police protection if they are breaking the law.
