Post-apartheid South Africa has seen an unprecedented rise and fall of mortality in less than two decades as a result of the HIV/AIDS epidemic and the subsequent rollout of free antiretroviral therapy (ART). Since the incidence of both was not equal for rich and poor, it is likely to also have affected disparities in health and survival chances by income. We use large nationwide surveys for 2001, 2007 and 2011 to obtain estimates of average income and mortality at the aggregate level of a municipality, and then to examine changes in mortality – and in inequality in mortality by income - over time. Using concentration indices to measure health inequality, we demonstrate that both the mean mortality level and absolute inequality in mortality by income rose rapidly until 2006, and declined again sharply since the rollout of free ART. Relative inequalities in mortality by income, however, remained fairly stable over the 2001–2011 period. The analysis of age-sex-specific mortality rates shows that it was in particular for adults aged 18–59 years that mortality and absolute inequality increased substantially between 2001 and 2006, followed by a rapid drop thereafter. These trends were far more pronounced for males than females. This means that the HIV/AIDS epidemic has taken a serious death toll, which was concentrated disproportionately among the poorest segments of the population and especially affected (older) males. While South Africa has been very successful in curbing the overall mortality trend since 2006, large disparities in survival prospects by income, race and gender continue to exist. Targeted efforts are required if it wants to further reduce the very unequal chances of living to old age for richer and poorer population groups of all ages.