The arrival at JNB pre covid could involve a significant queue for passport control, and that may be worse with temperature scanning potentially on exiting the plane, at immigration, on entering baggage reclaim and on exiting customs, so allow a good 3 hours after landing.
Cape Town departures are from the domestic terminal, but the transfer between terminals is an easy 3 minute indoor walk. You will get hassled by a large number of semi-official porters offering to push your trolley as you exit cusoms. They will take a polite "no thank you" as an answer if you wish.
Immediately on leaving customs, go up a level in the terminal lifts or escalators, (The baggage trolleys are escalator compatible). ATMs are on the next level up, and you need to be on the departure level anyway. Check in tends to be efficient at domestic, and an early afternoon flight to Cape Town is easily do-able, as long as the flight isn't delayed. SAA and BA between them have a dozen flights a day on the route. There are a number of LCCs as well. Mango and Kulula spring to mind, but Kulula is part of Comair, so equally affected by business rescue issues at present. If all goes well you will have time for a shower and meal in the lounge and be in Cape Town for mid afternoon. Unfortunately you can't add the Cape Town leg to your existing 241, since the voucher is not usable on franchise partners, so the risk of a missed connection is yours, not the airlines.
If overnighting in Joburg, consider an on airport property (The Intercontinental or the Park Inn being the choices) or any of a number of close by hotels with shuttles the Peermont Casino complex has 4 on site, the Protea is a good middle of the range choice or the Southern Sun for a more high end option. Another option is the Gautrain to Sandton. (On the opposite side of the terminal building to domestic departures) The Intercontinental is by far the easiest, maybe 150m from exiting the customs hall. Or a bit further afield the Misty Hills Country Club for the Carnivore Restaurant (a sister to the one in Nairobi.)
Airlink run a direct flight to Skukuza, where you could transfer to a lodge link flight, or pick up a car from Avis. There is also the option of a flight to KMIA (Nelspruit/Mbombela) from Cape Town.
For your return leg, I'd say upper deck, a window pair in the last row of either club cabin (direct aisle access for both).
Enjoy. Be warned that it is an addiction.