He also advised the countries to consider other measures if the situation continued.
Mr Obasanjo stated this while reacting to the xenophobic crisis through a letter to the president of the Inkatha Freedom Party, Mangosuthu Buthelezi, who is a leader of the opposition in South Africa.
Mr Buthelezi had publicly condemned the attacks and was last week booed off the stage at a rally in Johannesburg to discourage South African youth from xenophobia.
“For any African country to encourage or allow or not seriously sanction xenophobia against Africans in their country, it is a great disservice not only to the country where xenophobia takes place and the countries of the victims concerned, but also a great disservice to the whole of Africa and black race,” Mr Obasanjo wrote.
The former president, in the letter which was made available to journalists by his media aide, Kehinde Akinyemi, said there is a “need for fence-mending, reconciliation and wound-binding between South Africa and the countries whose citizens have been victims of xenophobia and Afrophobia in South Africa.
“As a suggestion, South Africa should send emissaries to the countries concerned to explain, apologise and agree on the way forward for mutual understanding, accommodation, reconciliation, and binding the wound to promote unity, concord, and brotherhood in Africa.”
Mr Obasanjo said, “repatriation of Nigerians from South Africa is obviously not a permanent solution, but at best it is palliative.” He said the hurt will remain for some time, adding that revenge is not a desirable solution.
“Mutual understanding and acknowledgement of what needs to be done on all sides are imperative and getting down to doing them is the solution that will serve Nigeria and South Africa and indeed Africa well particularly in this era of Africa Continental Free Trade Area opportunities.
“Nigeria and South Africa must stand together to champion African cause and to jointly shepherd African development, unity, cooperation, security, and progress to make the 21st century Africa’s century,” he wrote.