SQ JNB - MNL rt for ZAR 25,727 - US$ 1,960
 

Singapore Airlines has some good fares from Johannesburg to Manila in Business Class for ZAR 25,727.
Quite a few dates available in August and probably other months as well.
It seems it only is available directly on the SQ website.

MNL - JNB - CPT return also available for US$ 2,156 with more options,including 787-1000 and A350 combination. :)

Sample itinerary available at this fare:

Departing
15 AUGUST (WED)FlyingJNB 19:55JohannesburgO.R Tambo Intl
Terminal A
16 AUGUST (THU)FlyingSIN 12:20SingaporeChangi
Singapore Airlines · SQ 481 · Airbus A350-900Business (D)

Layover time: 1hr 30mins
16 AUGUST (THU)FlyingSIN 13:50SingaporeChangi
Terminal 2
16 AUGUST (THU)FlyingMNL 17:25ManilaNinoy Aquino Intl
Terminal 3Singapore Airlines · SQ 916 · Boeing 777-300Business (D)

Total travel time: 15hrs 30mins
Returning
22 AUGUST (WED)FlyingMNL 07:40ManilaNinoy Aquino Intl
Terminal 3
22 AUGUST (WED)FlyingSIN 11:20SingaporeChangi
Singapore Airlines · SQ 915 · 787Business (D)

Layover time: 2hrs 40mins
22 AUGUST (WED)FlyingSIN 14:00SingaporeChangi
Terminal 3
22 AUGUST (WED)FlyingJNB 18:40JohannesburgO.R Tambo Intl
Terminal ASingapore Airlines · SQ 482 · Airbus A350-900Business (D)

Total travel time: 17hrs