Note: Updated answer on 11 February 2017.
A South African consulate page in the US has this statement:
Travelers transiting through the following international airports are
exempted from/do not have to be in possession of transit visas, but
will be subjected to biometric capturing directly at the airport:
- OR Tambo International;
- Cape Town International;
- King Shaka; and
- Lanseria (Johannesburg)
Please note that the above-mentioned exemption
does not apply to deportees. Please also note that foreigners who are
utilizing land ports of entry to transit through the Republic of South
Africa and who are subject to South Africa visa control should apply
for and be issued with port of entry visas.
I haven't been able to find anything on the South Africa site, but the South African embassy in Australia had this outdated statement:
Transit Visa Requirements
Visa restricted passport holders who want to transit South Africa to
any one of South Africa's neighbouring countries, MUST apply for a
transit visa. The neighbouring countries are Botswana, Lesotho,
Mozambique, Namibia, Swaziland and Zimbabwe.
Passport holders who want to transit a South African port of entry
enroute to any other country, may do so without the need to apply for
a transit visa.
I found the same statement on a South African Airlines website.
Update from 25th August 2019 The South African embassy in Australia has since then updated their site and now has pretty much the same statement as the South African consulate page in NY above.
End finally, a user posted in the comments this dha.gov.za link, which is the official policy of the "Department Home Affairs, Republic of South Africa" and §11 states the very important details:
With effect from 18 December 2015 travellers, with the exception of
deportees, who transit through O R Tambo International Airport; Cape
Town International Airport; King Shaka International Airport and
Lanseria International Airport do not require transit visas as
contemplated in section 10B(4)(a) of the Immigration Act, 2002 (Act No
13 of 2002). However, transiting passengers will be subjected to
biometric capturing. Deportees transiting at any port of entry are
required to be in possession of a transit visa at all times and must