The second batch of 315 Nigerians returned from South Africa on Wednesday at about 7:22 p.m. at the cargo wing of the Murtala Muhammed International Airport, Lagos.
The evacuation which should have taken place on Tuesday was stalled due to delayed landing permit to Air Peace by the South African airport authority.
About 320 people were expected but five passengers were said to have been dropped as a result of documentation issues.
“They’re coming off the plane,” said Ibrahim Farinloye, spokesman of the National Emergency Management Agency, adding that he was not able to give an exact figure for the evacuees but he had been told there were 314.
A large crowd greeted the evacuees at the airport of the country’s economic capital Lagos after they disembarked around 9 pm (2200 GMT).
Last week nearly 200 other Nigerians were repatriated aboard a specially chartered plane following the violence that rocked Johannesburg and surrounding areas.
A series of deadly attacks on foreigners included many directed against Nigerian-owned businesses and properties.
Hundreds of shops were looted or destroyed.
Some 100,000 Nigerians are estimated to reside in South Africa, according to the Nigerian consulate in Johannesburg, which says however that it does not have exact figures.