South African citizens and permanent and temporary residents will be allowed to enter South Africa, whether or not they are travelling from or through a high-risk country, subject to the prescribed entry requirements (i.e. valid and negative COVID-19 PCR test result).
Entry into South Africa for foreign nationals is based on where the traveller has spent the previous 10 days.
If the passport of a foreign national traveller from a high-risk country indicates that they have spent 10 days or more in a low-risk country before departure to South Africa, they will be considered to be arriving from a low-risk country and subject to the low-risk entry requirements. (Note that this point was announced in Minister Naledi Pandor’s briefing on 30 September, but has not appeared in a government gazette as of yet.)
We are still awaiting clarity on how travellers can prove they have spent 10 days in a low-risk country in cases where there is not a passport stamp to indicate as much (e.g. passports are not stamped between EU countries).
Also note that transit through high-risk countries, where the traveller does not pass through immigration, is allowed, subject to the prescribed entry requirements. The restriction applies to travellers originating from a high-risk country.