The following lists events that happened during 1999 in South Africa.

• President:
  • Nelson Mandela (until 16 June).^[1]
  • Thabo Mbeki (from 16 June).^[1]
• Deputy President: Thabo Mbeki (until 16 June), Jacob Zuma (starting 16 June).
• Chief Justice: Ismail Mahomed.

January

• 14 – South African Police Service Captain Bennie Lategan who was investigating People Against Gangsterism and Drugs (PAGAD) is killed in a drive-by-shooting in Cape Town.
• 27 – Controversial youth drama series, Yizo Yizo debuts on SABC 1.

March

• 4 – BBC Prime was launched for the very first time in South Africa.
• 20 – The Azanian People's Liberation Army (APLA), the military wing of the Pan Africanist Congress (PAC), disbands.
• 24 – Allan Boesak, former Director of the Foundation for Peace and Justice, is sentenced to 8 years in prison for fraud.
• 31 – The Durban High Court finds Sipho Thwala guilty of 16 murders and 10 rapes and sentences him to 506 years in prison.

April

• 20 – Judge Edwin Cameron, high court judge and human rights advocate, announces that he is HIV positive.
• 23 – Makhaya Ntini, cricketer, is found guilty of raping a student.

May

• 29 – Cathy O'Dowd becomes the first woman to summit Mount Everest from both the north and south sides.

June

• 2 – The second democratic elections take place and is won by the African National Congress.
• 10 – George Bizos is awarded the Order for Meritorious Service, Class II, by President Nelson Mandela.
• 16 – Thabo Mbeki becomes the second President of South Africa.
• Watershed are signed to EMI Music South Africa and begin recording their first album In the Meantime.

August

• British children's television series Thomas the Tank Engine & Friends returns to airing on television in South Africa after a very long absence since its very last air on TV1 (now SABC 2). The series will now broadcast on M-Net as part of their K-T.V. children's block.

September

• 2 – A South African Air Force Alouette III helicopter crashes near Port Elizabeth, killing pilot Major K.A. Newman and seriously injuring two crew members.
• 10–19 – The All-Africa Games take place in Johannesburg.^[2]

October

• 22 – Henry Navigator, a 13,000 ton Cyprus bulk carrier, sinks off Bok Point about 35 km north of Cape Town.
• 23 – A South African Air Force Oryx helicopter crashes near Kroonstad, killing 10 people and injuring 14 others.
• Queen Elizabeth II and The Duke of Edinburgh visit South Africa.
• The Greater St. Lucia Wetland Park is declared a UNESCO World Heritage Site.

November

• 11 – UK children's stop motion animated series Bob the Builder begins on SABC 2 and was shown every Thursday.
• 15 – Afrikaans language television channel kykNET is launched.

December

• 3 – Government signs the final purchasing agreement in the arms deal and the loan agreement to pay for the equipment is signed by Finance Minister Trevor Manuel.^[3]

Unknown Date

• Statistics South Africa conducts a Survey of Activities of Young People.

• 14 January - Henco Pieters, future developer
• 25 January - Ndavi Nokeri, Miss South Africa 2022
• 16 February – Chloe Meecham, water polo player^[4]
• 20 February - Boohle, singer
• 3 March - Sphephelo Sithole, soccer player
• 2 April – Elaine, singer and songwriter
• 26 April - Laura Wolvaardt, cricket player
• 22 May - Bongeka Gamede, soccer player
• 11 June - Paballo Mavundla, actor
• 29 November - Kamo Mphela, dancer and singer
• Masego Kgomo, muti murder victim. (d. 2009)

• 10 January – Gavin Relly, businessman and Chairman of Anglo American.^[5] (b. 1926)
• 26 May – David Millin, 78, movie director, producer, and cinematographer (b. 1920)^[6]
• 27 July – Simon "Mahlathini" Nkabinde, mbaqanga singer (b.1938)
• 15 November – Pieter van der Byl, politician (b. 1923)