President Muhammadu Buhari on Monday called for the immediate voluntary evacuation of all Nigerians wanting to return home, and Air Peace offered free flights last week.
At least 640 Nigerians have signed up to take free flights home from South Africa after xenophobic attacks on foreigners
Private Nigerian airline Air Peace plans to operate two flights with Boeing 777 aircraft, the first leaving Lagos late on Tuesday to return on Wednesday with evacuees.
The plane can carry roughly 300 passengers.
In the latest of periodic xenophobic violence in South Africa, deadly riots last week in Pretoria and Johannesburg killed at least 10 people including two foreigners and targeted foreign-owned businesses.
Retaliatory attacks in Nigeria forced South African businesses to shut doors for several days, and South Africa temporarily closed its embassy on safety fears.
Buhari will visit South Africa next month to address the attacks and seek a solution.
