So, factoring in your travel days, you will have about 12 days on the ground?
I would arrive in JNB and then go to the Kruger Park for a few days. There are various camps that cater to various price points. Or, you can rent a vehicle, and stay at the SANParks accommodation and drive yourself around the park.
While you are there, and visas are not an issue, you can drive over to Maputo for about two days and experience another taste of Africa - hot, humid coast and plenty of seafood prepared in a typical Mozambique style: spicy and hot.
Then, get back to JNB and go to Cape Town - lots of wine farms, shark cage diving, surfing or even hiking up Table Mountain.
Or, instead of flying down and you get a good deal with the rental (unlimited mileage), you can of course drive down over, say three days - I have done this on several occasions. Instead of the usual N1 route, I have gone via Kimberly - you can stay at the Kimberly Club which is charming.
You can then join the N1 route, or continue west and follow the route down the west coast.

That way, you can enjoy the wildlife, some exotic coastal experience, the interior and the opposite coast (west coast), maybe some diving and finally, great food and wine.
Emirates fly out of CPT, so if you fly into JNB, you fly out of CPT, making your flights easier to plan.