The temporary restriction on non-essential travel to the EU which was implemented since 17 March has now been prolonged and is valid until 15 June 2020.
More information to the new EU-Regulation can be found here.
Frequently asked questions can be found here.
Further information for travelers to Germany can be found on the website of the Foreign Ministry:
The German Embassy and the Consulate General are aware that South African Authorities currently require from their own nationals who want to leave the country a
“… Proof that confirms your admissibility in the form of a letter from the embassy or other diplomatic / consular representative of your country of normal residence, confirming your right of residence in that country and that you are permitted to return thereto under the current circumstances. If returning by road or connecting flights, the proof submitted to us needs to include each transiting countries permission for your travel.”
Please note that the German Missions abroad are not in a position to issue such letters of admissibility. However, for serving the purpose, you may find the confirmation useful, which you can download here.