Although Cape Town is well away from the areas of the country where Malaria is prevalent, if you are taking a lengthy tour of the country, and the city is just one stop off, it is a good idea to take appropriate precautions. You should always take out adequate medical insurance prior to travel, as hospital treatment in South Africa as a whole can be quite pricy, and medical repatriation to the UK is very expensive.
The hospitals in the city are of an excellent standard, and offer a full service for travellers