The South African government congratulated Southern Sudan on the "peaceful and well concluded" referendum, the department of international relations and co-operation (DIRCO) said on Wednesday.
The people of South Sudan voted in a referendum last week to decide whether they would remain part of a united Sudan or form a new, independent state.
The week-long referendum was concluded on Saturday.
"South Africa would like to congratulate the people of Southern Sudan, the Southern Sudan Referendum Commission and Bureau on the peaceful and well conducted referendum," department spokesperson Clayson Monyela said in a statement.
"Furthermore, South Africa would like to commend both President Al-Bashir and First Vice President Salva Kiir on the personal leadership and courage they have shown in facilitating a conducive and peaceful environment for citizens to participate freely and without fear in casting their ballots."
South Africa had sent a team of 35 people, including members of parliament and civil society, to observe the referendum "to assist in ensuring a conducive environment for a credible, free and fair referendum".
The country's support was based on its role as chair of the African Union Committee on Post Conflict Reconstruction and Development in Sudan.
The steps taken in the Sudan was a positive sign of further developments in the country and for the Horn of Africa region and entire continent of Africa, said Monyela.