The 178 Nigerians arrived in Nigeria on Wednesday evening and were received by the acting director in the southern African affairs division, Chuks Chikezie Jonathan.
"The aircraft conveying them arrived at Murtala Mohammed International Airport, Lagos, at 9.23pm on Wednesday September 11 2019," the Nigerian ministry said.
At least 12 people were killed in attacks on foreign businesses in Johannesburg and Pretoria in the past few weeks.
Onyeama applauded Air Peace owner Allen Onyema for the offer of free flights for Nigerians out of South Africa. Onyeama said the second flight would happen soon, once necessary arrangements were made by Nigerian missions in South Africa.