I did JFK-JNB-VFA back in Sept of last year. When you arrive at JNB you need to go to the international transit area (as you mentioned). There is a desk where they look at your passport and stamp it with a transit stamp. There could be a short line here (few people in front of me when I arrived at the same time). You don't need to go through customs. Then you need to go through security again (once again short line of a few people) and proceed to your gate.

90min should be plenty if your flights arrive/depart ontime. The only thing I would caution is that if i recall correctly it's a bit of a walk from the arrival gate to the immigration / security checkpoint and back to the gates, so if you are a slow walker, etc just be aware of that. Maybe 10-12min walk total at a normal pace.