If you want to drive across the border from Namibia into neighbouring South Africa, then you need permission from your hire car company in the form of a letter including the vehicle registration number and chassis number. 

This must be presented at the border post, and a permit will be issued which must be carried at all times. 

There may be a fee payable as well at the border post. 

In terms of paperwork, you can expect to spend about 15 minutes walking from Immigration to Customs, and having your passport checked and stamped, but overall, the procedure is surprisingly painless. 

There are 2 major border posts when crossing into South Africa:

Noordoewer (open 24 hours) - when travelling to Cape Town and the Western Cape.

Nakop (open 24 hours) -  when travelling to anywhere else in South Africa.