The ship sailed from Walvis Bay last Friday and arrived in Cape Town on Sunday. The six passengers had flown to Cape Town from Istanbul on the same plane as a cargo ship crew member who later developed Covid-19 symptoms.
The ship's quarantine was finally lifted on Wednesday when the six passengers - who were taken off the ship - tested negative.
Transport minister Fikile Mbalula said on Friday the German government had sent four empty planes to collect passengers and fly them home.
“The crew will not be permitted to disembark but will await the arrival of the German nationals, who will be escorted from the AIDAmira and on to the plane,” said a transport ministry statement.