South Sudan became independent July 2011, but since then relations have deteriorated with numerous clashes along their disputed border.
It has also halted oil production amid a dispute over sharing revenues.
The South Sudanese opted to split from the north last year, following a peace deal in 2005 which ended decades of civil war in which some 1.5 million people died.
The countries have also failed to reach agreement on borders and accuse each other of backing militia groups.
Mr Mbeki spoke to reporters after the first meeting in a fresh round of talks in Ethiopia's capital, Addis Ababa, to resolve some of these issues.
He said both sides had pledged to "refrain from launching any attack, including bombardment".
Earlier, UN Secretary General Ban Ki-moon had voiced his concern about the slow progress of the negotiations.
"The moment has come for the leaders of both countries to make the necessary compromises, once again, that will guarantee a peaceful and prosperous future for both nations," he said a statement.