Colonialism occured on many countries and continents at various times in history and to varying degrees of brutality. In some cases, such as the USA and Australia, systematic genocide was visited upon their indigenous populations, while elswhere, examples of softer oppresions were applied. In South Africa specifically, softer oppresion in the colonial era occurred and no genocide (as defined by the systematic wholesale slaughter of ethnic groups) happened. Prior to the colonial era, genocidal actions were common, with the Mfecane and eradication of Koi Bushmen by black African hordes as they marched South and West in colonial expansion.
The Holocaust was different in that a vast people defined only by their religion, were slaughtered on an industrial scale on the back of a racist ideology. Very different. European Jews were citizens of the country in which they were wiped out for being of the Jewish religion. No comparison can be made excepting by anti-semitic racists.