I suppose the best way to make this happen is in the run up to the 1994 elections.
A few factions stood against ANC control of the country. The Zulu nationalist Inkatha movement, led by Chief Buthelezi, were engaged in a set of battles with the ANC in KwaZulu Natal and were broadly successful in maintaining control over a good chunk of territory in the Northern and more rural central parts of the province.
At the same time, the Afrikaner Volksfront, a right wing militia, was mobilizing a large number of Afrikaners (up to 60,000 I think) under the leadership of trained ex-SADF leadership. And then you have to consider the SADF itself; nominally in allegiance to the government, but ideologically, a good many of its members weren't so happy with the way things were going.
And then, you get the issue of the Bantustan leaders, who in many cases did not want to give up power. Mangope in OTL was deposed in a coup, but had he retained power, he could have caused issues in the Northwest Province, while in Ciskei, again, it was a strike by government workers that took their leaderdown. Both of those events could have turned out quite differently.
If you don't get the Inkatha Party and the Freedom Front to run in the elections and lend them legitimacy, you have a real problem on your hands. In OTL, they did so, and things became peaceful (although, crime still spun out of control) afterwards. The new state was fragile. The SADF was about to fire a lot of people, many of which had a lot of wartime experience during the 80s and became quite adept at fighting a guerilla style war. Its likely that the AVF would have swelled under this scenario, and the Inkatha forces would have received even more clandestine support.
Add to the equation the issue of tribalism within the ANC, as the Xhosa dominated executive committee (Tambo, Mandela, and Mbeki were all Eastern Cape Xhosas, if I remember correctly). The highest ranking Zulu in the ANC for much of its post liberation history (although I'm not sure if it was the case in 1994), and arguably one of their most important symbols during the fights with Inkatha, was Jacob Zuma, who we know to be hilariously corrupt. While I don't think its likely, if he defects to Inkatha (presumably because he either listens to the council of a Chief he respects who likes Inkatha, or because one of the Indian businessmen who gives him and his family money tells him to), it could cause South Africa to fracture further on Xhosa-Zulu lines. The traditional leaders of South Africa (Chiefs and Kings) were ideologically incompatible with the Marxist leaning elements in the ANC, and it took Mandela's pragmatism to keep that issue from getting out of control. Remove him, and things could break down quite different.
So there are many ways to bring about a Civil War in South Africa in the run up to the end of Apartheid.