The second batches of Nigerians have departed the OR Tambo International Airport, Johannesburg, for the Murtala Muhammed International Airport, Lagos.
About 319 persons were evacuated by Air Peace at about 2:58p.m.
An official of the Ministry of Foreign Affairs, Kimiebi Ebenfa, confirmed on Wednesday.
The first flight had brought back 187 Nigerians out of the 313 scheduled for the evacuation last Wednesday, following the xenophobic attacks against foreign nationals in SA.
The Consul-General, Nigerian High Commission in South Africa, Godwin Adama, had disclosed that the number of registered Nigerians had risen to 1,004, adding that the technical issues faced during the first evacuation were being addressed.
817 Nigerians were awaiting evacuation.