I managed to track down a used KTM 640 Adventure privately. I spent a week or so pounding the Cape Town streets on foot, visiting dealers before I found this bike, which was unadvertised. The main area for bike sales / servicing is located a couple of blocks either side of the corner of Bree Street and the Strand in the Cape Town CBD. You will find KTM, Honda and Kawasaki dealerships (plus a few non dual sport dealerships) all within walking distance of each other. There is also a BMW dealership near the V & A Waterfront and a Yamaha dealership about 10 minutes walk from the area.
However I found in all the dealers that their stock of used dual sport bikes capable of doing a cross Africa trip to be remarkably limited. If you have the cash, buying new should be no problem, although KTM have a waiting list on new 640 Adventures (and possibly 950s), and Honda don't stock any real dual sports bigger than the XR400 (although they do carry the TransAlp).
Hope that helps