I've flown round-trip between PTY and JNB several times. My recollection is that there is no transfer desk, but you will need a boarding pass at the light-security "re-check" point. If SA does not give you a CM boarding pass (I predict they will, and I also predict you will not be able to produce a mobile boarding pass for CM), you can probably just show a print-out of your itinerary.
I'll be flying JNB-GRU-PTY next week; I'll confirm the details.