SANDF brigadier general, Xolani Mabanga said there had been casualties on both sides.
Unconfirmed reports say that 9 South African soldiers were killed in the skirmish with rebel soldiers.
General Mabanga said the contact between SANDF members and Central African Republic rebel forces took place on Saturday on the outskirts of the capital, Bangui.
South Africa deployed 200 soldiers to Central Africa in January to support the poorly trained, ill-equipped government troops following an offensive launched by the Seleka rebel coalition in early December.
The SANDF deployment went to CAR earlier this year on instruction from President Jacob Zuma, who is also Commander-in-Chief of the South African military
It was reported on Sunday night that CAR president, Francois Bozize, had fled the capital and that members of his family had sought refuge in neighbouring Democratic Republic of Congo.
Rebels signed a peace deal in January allowing Bozize to see out his term which expires in 2016 but soon accused him of not sticking to the dea