They landed around 7.22pm at the cargo wing of the Murtala Muhammed International Airport, Lagos.
The evacuation, which should have taken place on Tuesday, was stalled due to the delayed issuance of landing permit to the Air Peace aircraft by the South African authority.
About 320 people were expected but a few passengers were said to have been dropped over documentation issues.
The Nigerians had departed the O. R. Tambo International Airport, Johannesburg, for the Murtala Muhammed International Airport around 1pm.
The first flight had brought back 187 Nigerians out of the 313 scheduled for evacuation last Wednesday.
The Consul-General, Nigerian High Commission in South Africa, Godwin Adama, had said the number of Nigerians willing to leave had risen to 1,004.
The Chairman of Air Peace, also said the plane left a few minutes after noon local time (1pm Nigerian time).
Onyema said some Nigerians had been stranded in South Africa for over four years.
He said, “I felt our country was being insulted and it was unacceptable to me. Accusing Nigerians is like saying we are all criminals.
“While I’m not supporting crime, I feel the earlier we start addressing the stereotyping of Nigerians as criminals, the better for us.”
Onyema said the airline’s crew for the evacuation refused to take allowances for the trips as their way of showing patriotism.
He said the airline was carrying out the evacuation without expecting any payment from the Federal Government.
The Chairman, Nigerians in Diaspora Commission, Mrs Abike Dabiri-Erewa, said the returnees would be profiled according to their states of origin and their governors would complement the Federal Government’s efforts towards integrating them into the society.
“When they settle down, their governors will get involved,” she added.
Dabiri-Erewa said the Nigerian High Commission in South Africa was working to ensure that the hitches in the evacuation were removed.
She, however, stated that the date for the next evacuation was still unknown.
The Governor of Lagos State, Babajide Sanwo-Olu, who sent delegates to receive the returnees, gave each of them N20,000.
Unlike the first evacuation, journalists were barred from covering the arrival at the tarmac as security officials were deployed with sniffer dogs to stop them from reaching the area.
One of the returnees, Chukwuekwu Okom, from Delta State, said Nigerians were constantly being harassed by South African police.
Okom said he was lucky to have survived and returned to Nigeria.
He said, “I will never go back. I spent six years in South Africa and came back with nothing, but I thank God that I survived.
“Things were so tough that I couldn’t pay my rent, I lived on the street for many months. I am back now, I will rather die here than go back.”
Olanrewaju Wasiu from Ikorodu, Lagos State, simply said he was happy to be back home.