update (05 July 2016): According to Tourismupdate.co.za, the situation at OR Tambo International Airport (JNB) in Johannesburg has reportedly eased although there are still queues. The Department of Home Affairs has stopped a number of biometric sets, which has made a big difference to the situation.
Both outbound and inbound travellers at OR Tambo International Airport (JNB) in Johannesburg are advised that South Africa's Department of Home Affairs has changed over to the biometric system. This causes massive delays as capturing biometrics is taking the immigration officials significantly longer to process passport holders. Delays are currently taking up to 2+ hours. (see the comments in the embedded post for updates regarding the delays!)