What sort of fares are you getting? The lowest published fares (which you can always get directly from the airline) are about £514 for JNB and £559 for CPT (plus tax). There's lots of availability in May at those levels, at least on BA which is the only place I've looked.
IME, these days you don't save very much if anything on most long-haul routes by going to other sources - a tenner or two here and there per person. Normally, Travelocity and Opodo are worse channels on which to book than going straight to BA because they add on fees which BA doesn't if you book online with them.
Is that consistent with what you've been finding?
If you need to get the lowest possible price for every ticket, one trick is to try pricing for one passenger rather than 4. You might for example be able to get one seat at the lowest price, and then pay the next level of fare for every one else.