Despite the end of apartheid in 1994, relations between the two countries have been severing due to competing economic and cultural influence, and various diplomatic disputes including xenophobic riots and violence in South Africa targeting Nigerians.

In June 1994, Nigeria's military ruler, General Sani Abacha arrested and sentenced for execution 40 political opponents including former Nigerian head of state Olusegun Obasanjo as well as Chief Moshood Abiola.

Mandela sent Archbishop Desmond Tutu and then Deputy President Thabo Mbeki on successive missions to Nigeria to lobby for the release of Obasanjo, Abiola and nine others.

However, one of South Africa's first experiments with quiet diplomacy failed when in November 1995 Abacha moved ahead with the execution of the nine Ogoni leaders including Ken Saro-Wiwa.

After which South African president Mandela then publicly criticised General Abacha for human rights abuses and personally pushed for a two-year suspension of Nigeria's membership in the Commonwealth of Nations.

On 29 March 1995 Wole Soyinka, leader of an exiled Nigerian democratic movement, attempted to hold a conference in South Africa.

The attacks instigated retaliatory violent reactions on South African businesses in Nigeria as many condemned the xenophobic violence taking place there.

In response, the South African President Ramaphosa, made an apology to Nigeria in 2019 through his envoy Jeff Radebe, stating that he was ashamed of the violence towards Nigerians.

He said, "The incident does not represent what we stand for," adding that South African police would "leave no stone unturned" in bringing those involved to justice.

At the conference, it was noted that Oando, an energy conglomerate based in Lagos had recently been listed on the Johannesburg Stock Exchange and the Nigeria-based Dangote Group had invested a record $378 million in South Africa's cement industry.

Nigerian businesspeople have expressed concern over the pace and perceived rapid expansion of South African business interests in the country.

For example the above mentioned issues of xenophobia and rigid visa-regimes raised red flags in the bilateral relations between Nigeria and South Africa.