"All non-essential personnel and families attached to the South African embassy in Cairo will be temporarily withdrawn until the situation allows for their return," spokesperson Clayson Monyela said on Thursday.
The embassy would however remain open and continue rendering consular assistance to South Africans in Egypt.
Monyela said government had observed with concern the suspension of the Constitution in Egypt and the "removal from office of a democratically elected president Mohamed Morsi".
"Instability in Egypt may have far-reaching consequences on the already precarious situation in the country, as well as the North African region and Middle East."
Armed forces overthrew Morsi on Wednesday, declaring that he had failed the Egyptian people. Morsi was toppled just a year after he was elected as Egypt's first freely elected president.
Monyela said South Africa was opposed to all forms of unconstitutional change of government, in line with the African Union Constitutive Act.
'Legal framework'
"We strongly encourage all Egyptians to resolve the present crisis through inclusive dialogue within the relevant national legal framework that seeks to consolidate the democratic achievements made by the Egyptian people in January 2011."
Monyela said South Africans intending to travel to Egypt should reconsider doing so.
Meanwhile, the African Union is likely to suspend Egypt from all its activities.
The AU source, who asked not to be identified, told Reuters on Thursday that members of the AU's peace and security council would meet on Friday and were likely to implement the AU's usual response to any interruption of constitutional rule by a member state.
"The belief is that the doctrine will be applied, which is suspension for any country where an unconstitutional change has taken place," he said.
In March, the AU also suspended the Central African Republic after rebels overthrew the government there.
Ramtane Lamamra, the AU commissioner for peace and security, told Reuters in the Ethiopian capital where the AU is based that the council would discuss Egypt's situation at the Friday meeting.
"We intend to dispatch a mission and urge the Egyptian authorities to establish dialogue," Lamamra said. – Sapa, Reuters