There's no direct link between the secure arrival area of Terminal A and the secure departure area of Terminal B, so you'll have to pass through Customs and Immigration if O.R. Tambo is your first stop in South Africa and you're connecting to a domestic flight.
The Protea Hotel Transit is in the International Terminal. There are also several options outside the terminals if you need to rest before continuing your travels by car. The Intercontinental is just a few steps from the Arrivals exit and has a pool, gym and spa. There's a City Lodge hotel with a pool close to the airport parking.