The Nigerian government began repatriating more than 600 of its citizens from South Africa following a series of xenophobic attacks.
Riots in Pretoria and Johannesburg killed at least 12 people in attacks target towards 1,000 foreign-owned businesses.
Private Nigerian airline Air Peace volunteered to fly people for free back to Lagos on Wednesday.
A second flight is expected to depart this week with 640 Nigerians in total fleeing the country.