African migrants in the South African capital, Pretoria, were urged to exercise "heightened vigilance" during an anti-illegal immigration march, amid fears of xenophobic attacks.
Ghana's high commission advised its nationals to close businesses and keep a "low profile", while the head of the Nigerian Union of South Africa told its members to remain indoors. Another march is due on Wednesday in Johannesburg.
Anti-migrant sentiment has gained political currency in recent years with some believing foreigners are taking jobs and unfairly benefiting from public services.
But the president said citizens should not allow their concerns to "breed prejudices and hatred towards our fellow Africans".
Condemning recent attacks on foreigners, President Cyril Ramaphosa used his Freedom Day address on Monday - marking the country's first democratic elections in 1994 - to also remind his country of their debt to other nations on the continent in supporting their struggle against the racist system of apartheid.
