And troops and civilians still in the country are in danger of revenge attacks.
South Africa began its formal relationship with the country in 2006 when it agreed to work with the government of President François Bozizé. This agreement was renewed last year. The personnel who were sent as part of this deal were the ones who fell under attack last weekend.
And it was the presence of these troops, along with complaints such as a lack of pay for rebel soldiers and the release of prisoners, that led to the collapse of the unity government and the coup, said Robert Besseling, deputy head of African forecasting at Exclusive Analysis.
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In peace talks in January between the rebels under Michel Djotodia and the government, one of the conditions for a deal was the withdrawal of South African troops, he said. "And now, given that they [the South African troops] physically defended the president, their situation in the Central African Republic has drastically changed."
If the members of the defence force did not manage to leave the country quickly – they are asking the French forces controlling the local airport for assistance in this regard – then Djotodia would probably force them out, Besseling said.
"There is also a high risk of retaliatory attacks on South African troops and civilians that are still there," he said. Many of these civilians had contracts to extract oil, uranium and gold in the country, but would likely lose these.
The probability is that the defence force will rapidly withdraw from the country and then ask the African Union (AU) to sanction some sort of military intervention there, he said.
South Africa's position as head of the AU would give this request some force. But because Bozizé came to power in a coup 10 years ago, and because of the silence of most other countries regarding Djotodia's coup, this request would probably be turned down, Besseling said.
Having backed the wrong side, South Africa would be left with no presence in the Central African Republic. "They will have no influence in the country now," he said.
François Misser, a French journalist who reports on the country, said that the South African intervention was doomed because it did not understand local conditions.
Djotodia was a civil servant in the former government and became a diplomat in the new one. The BBC reports that his command of languages made him an ideal diplomat, and he was sent to work in Darfur. It was there that he met the fighters that would form the basis of his Seleka alliance. Revolution soon followed. In 2006 he was jailed for a year in Benin for his role in trying to overthrow the government.
In a radio interview this week he promised to hold elections within three years.