FAQ: I work in Johannesburg where I bought a townhouse to stay. My wife and three children still stay in Umtata, my hometown, where I have my main home. Will the sale of my townhouse qualify for the primary residence exclusion when I move back to Umtata?

You will have to choose which of the two residences is to be regarded as your primary residence. If you choose the townhouse then the proceeds from the sale of the townhouse would qualify for the primary residence exclusion.
However, should you later dispose of your house in Umtata, any capital gain or loss on its disposal would be subject to CGT for the period that you stayed in your townhouse. This follows from the fact that a person may not claim a primary residence exclusion for more than one residence at a time (paragraph 45(3) of the Eighth Schedule).