President Muhammadu Buhari on Monday received a delegation from President Cyril Ramaphosa at the presidential villa in Abuja.
The Nigerian leader had earlier sent a special envoy to his South African counterpart over the attacks on Nigerians.
Jeff Radebe, who led the team, tendered an apology to Nigeria on behalf of the government and people of South Africa.
Radebe apologised for what he called “acts of criminality and violence” that recently occurred, adding that “such do not represent our value system, nor those of the larger number of South Africans”.
Rauf Aregbesola, minister of interior and Abba Kyari, chief of staff, were among those who received the envoy.