Advice against all but essential travel was imposed against South Africa, Namibia, Zimbabwe, Botswana, Lesotho and Eswatini "based on the current assessment of Covid-19 risks".
A temporary ban on commercial and private planes travelling from the six countries will come into force until 4am Sunday (28 November), where passengers will then be required to book and pay for a government-approved hotel quarantine facility for 10 days.
The restrictions were described as a "hammer blow" by the African Travel and Tourism Association (Atta).