Hi Craviec,
Yes, your hours in South Africa will count.
In order to fly in South Africa on a JAA (or other "Foreign" license), you need to do a foreign license validation or conversion. It is easier to do a validation than a conversion (only one written exam- airlaw), two lectures, (one on density altitude and flight planning, and one on our airspaces) and a PPL flight test, including a cross country flight. This validation is valid for 5 years, provided your original license and medical remain valid. The foreign license validation has to be done through a Part 141 flight school.
You can complete most of the process before you set foot in South Africa, so you can maximize your flying time in the country. Perhaps we will even see you in Richards Bay
All the best