"We stopped them from flying to Syria and the airline concerned was also informed and they were refused access," said Hangwani Mulaudzi, spokesman for the Directorate for Priority Crime Investigation, widely known as "the Hawks."
The arrests were made on Saturday and the three men and one woman will appear in court on Monday, two in Johannesburg and two others at the Kagiso Magistrates Court west of Johannesburg, Mulaudzi said.
Foreign nationals have flocked to Syria to fight for or against Islamic State, an ultra-hardline Sunni group that has also carried out deadly attacks worldwide.
Security officials say there are no known militant groups operating in South Africa, but Britain and the United States warned in June of a high threat of attacks against foreigners in the country's shopping malls.
Some analysts say economic hardships could be a catalyst for radicalizing South Africa's small Muslim population.