South Africa has MANY places that regularly record over 40 degrees, that temperature is really nothing special. Even Cape Town, which has a Mediterranean Climate (and therefore relatively mild) recorded a new high of 42 degrees C in March 2009. Durban has also recorded 42C one September. Grahamstown in the Eastern Cape, usually a fairly mild area, even reached 42C in 1999, and Cradock in the ECape records 40s often. Messina, Mafikeng, Kimberly etc etc often do as well. Upington, in the Northern Cape, often has the Countries highest temperature (and is one of the 5 sunniest cities on Earth) with 40s very regular indeed in Summer, and a January high of 46 officially recorded. The North Eastern Areas of Limpopo or Mpumalanga are especially warm. Even in Winter, the Lowveld (i.e. The NE areas) has average daily highs which are hover between 25C and 30C, and frequently reach more than 32 degrees C (90F). In Summer these areas are frequently over 40 degrees C (often for several days per week), and feel especially warm due to high humidity. There are anecdotal reports of 52C from Komatipoort in November of 2006. However, the official record for the highest temperatures in South Africa belong to the Richtersveld National Park - Northern Cape (bordering with Namibia). This park has recorded an official temperature (recorded Meteorologic-ally. I.e. In Shade, 1m above ground and shielded) of 53 Degrees Celsius (127.4 Fahrenheit), making it one of the hottest areas on the planet. It is also one of the driest, receiving less than 2 inches of rain per year (usually one day of rain per year).
The hottest Place In South Africa is the Northern Cape, temperatures close to the Namibian border have been recorded in excess of 40 Celsius. The capital of the Northern cape is Kimberley.
Musina and Upington if you look at the general averages throughout the country.