"The incident does not represent what we stand for," envoy Jeff Radebe said, adding that South African police would "leave no stone unturned" to provide justice.
South Africa apologized to Nigeria over a series of xenophobic attacks which escalated tension between the two countries.
A special envoy from South Africa apologized to Nigeria’s President Muhammadu Buhari Monday.
"The incident does not represent what we stand for," envoy Jeff Radebe said, adding that South African police would "leave no stone unturned" in bringing those involved to justice.
"President Buhari responded to profuse apologies from the South African president, pledging that the relationship between the two countries will be solidified," a statement from President’s office said.
South Africa's President Cyril Ramaphosa last week said, "We are very concerned and of course as a nation we [are] ashamed because this goes against the ethos of what South Africa stands for.”
Nigeria started Wednesday the repatriation of more than 600 of its citizens from South Africa after attacks broke out in the beginning of September.
The repatriation came after a cycle of violence burst out in Johannesburg on Sept. 1 leading to attacks on some 1,000 foreign-owned businesses and shops, and killing 12 people while injuring many.
The nationalities of those killed have not been confirmed yet, but Nigerians, Ethiopians, Congolese, and Zimbabweans were assaulted, according to local media.
Many videos of the attacks circulated on social media, triggering international outrage and calls for a boycott of South Africa.
The attacks on foreign nationals and their businesses were not the firsts of their kind in the Southern African country. Before 1994, migrants used to face discrimination and violence, as the nation transitioned from South Africa's National Party government which ruled the country since 1948 and advocated the apartheid system to the African National Congress (ANC), contrary to expectations, the frequency of xenophobia increased.