I understand that it wasn't feasible to develop cities in the dense jungles of central Africa, but around this jungles there were many cities and kingdoms, except for South Africa, why?
I guess it depends on what we count as a city.
Dr Karim Sadr of Wits university in South Africa found that 15th-19th century Tswana settlements at the Suikerbosrand hills near Johannesburg were much larger than previously thought.
Does that count as a city? Honestly, I don't know. According to Dr. Sadr, there may have been between 750-850 homesteads at the SKBR site. We should remember that Tswana homesteads in the 18th century would not be like the modern nuclear family. It would include the paterfamilias, elderly dependents, primary wives and possibly 2nd and third wives, plus children. So, each homestead could have between 5 and ~15 people in it. But it's not clear that all of those homesteads were occupied at the same time.
So, if we assume the average population per homestead is 8, and 750 homesteads were occupied at the same time, that gives a settlement of ~ 6,000 people. Which is comparable to Mapungubwe and some of the other Zimbabwe sites.
If we assume that only half of all homesteads were occupied at the same time, or we assume that average homestead populations were smaller, then we might arrive at smaller total population estimates circa 2,500-3,500.
It then becomes a question of what population is necessary to deem something a city. Is it a question of economic specialization. To really determine whether there were specialized full-time merchants, blacksmiths, administrators, etc, might require further archaeological investigation as well as linguistic and ethnographic study.
Furthermore, Dr Sadr's discovery comes from the application of this LiDAR technology to a specific site. Further use of LiDar to sites in Xhosaland, Zululand, and other areas might or might not result in further discoveries of similar extensive settlements prior to the 19th century. It definitely warrants further investigation.
Just to clarify, do you mean on the territory of the modern Republic of South Africa specifically? Because there were large cities in Southern Africa such as Great Zimbabwe and Swahili coast cities in modern Mozambique like Quelimane and Sofala.