Trends in socioeconomic-related health inequalities is a particularly pertinent topic in South Africa where years of systematic discrimination under apartheid bequeathed a legacy of inequalities in health outcomes. We use three nationally representative datasets to examine trends in income- and race-related inequalities in life expectancy (LE) and health-adjusted life expectancy (HALE) since the beginning of the millennium. We find that, in aggregate, (HA)LE at age five fell substantially between 2001 and 2007, but then increased to above 2001 levels by 2016, with the largest changes observed among prime age adults. Income- and race-related inequalities in both LE and HALE favor relatively well-off and non-Black South Africans in all survey years. Both income- and race-related inequalities in (HA)LE grew between 2001 and 2007, and then narrowed between 2007 to 2016. However, while race-related inequalities in (HA)LE in 2016 were smaller than in 2001, income-related inequalities in (HA)LE were greater in 2016 than in 2001. Based on the patterns and timing observed, these trends in income- and race-related inequalities in (HA)LE are most likely related to the delayed initial policy response to the HIV epidemic, the subsequent rapid and effective rollout of anti-retroviral therapy, and the changes in the overall income distribution among Black South Africans. In particular, the growth of the Black middle class narrowed the HA(LE) gap with the non-Black population but reinforced income-related inequalities.