Some 200 South African troops had been stationed in the country's capital Bangui to support government forces.
President Jacob Zuma (pictured) said the deal between the countries had become void with the ousting of Francois Bozize, who is now in Cameroon.
Mr Zuma was facing anger after 13 South African soldiers died and another 27 were injured in the rebellion last week.
He announced the withdrawal at an emergency regional summit on CAR, during which African heads of state refused to recognise the rebel leader.
Michel Djotodia declared on 25 March that he would rule by decree after his Seleka rebel group ended President Bozize's decade-long rule.
Image: © Getty
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