Nigerian President Muhammadu Buhari is expected to visit South Africa in October to "reinforce strong bonds", following a spate of attacks against West Africans.
The Presidency said on Saturday that the two countries would "jointly develop responses to challenges affecting people and businesses in South Africa and Nigeria".
The South African embassy in Lagos, Nigeria, closed its doors on Wednesday after it came under attack.
Some South African businesses operating in Nigeria, including MTN, also closed until further notice after they were attacked.
Poor diplomatic relations between the two African countries, comes after Nigeria introduced plans to evacuate its nationals in South Africa following a wave of attacks on foreigners, including Nigerians.
President Cyril Ramaphosa held discussions on Friday with Ambassador Ahmed Rufai Abubakar, the special envoy of Buhari.
Presidency spokesperson Khuselo Diko said the special envoy's visit to Pretoria followed a recent meeting between Ramaphosa and Buhari in Yokohama, Japan, on the sidelines of the Summit of the Tokyo International Conference on African Development.
"In [the] discussion, the special envoy conveyed President Buhari's concern at recent events in South Africa, in the context of the strong and cordial relations that characterise the interaction between the two countries," said Diko.
Diko said Buhari conveyed his "commitment to the values of prosperity and the advancement of Africa that are shared by South Africa and Nigeria".
"Nigeria stands ready to assist South Africa in establishing the root causes of and developing sustainable solutions to the challenges concerned. President Buhari has undertaken that where challenges emerge in Nigeria, the Nigerian government will act against lawlessness and the targeting of South African assets in Nigeria."
Ramaphosa reaffirmed SA-Nigeria relations as "firm and strong" and said the two partners were resolute in their shared commitment to build an Africa at peace with itself and others.