Oakhurst ancient San genomes cluster with southern San and show basal divergence from all other humans. Southern San gene pool formed over 10,000 years ago and persisted without non-southern African input until 1,300 years ago. No detectable gene flow from northern or central San into Oakhurst inhabitants over 9,000 years. Modern ‡Khomani San and Karretjiemense share direct IBD segments with 1,300-year-old Oakhurst San. All contemporary San and Khoe carry at least 9% non-San admixture obscuring ancient structure. Pastoralist East African ancestry arrived in South Africa after 1,300 cal BP. Bantu West African ancestry admixed later around 800-500 years ago. Female-biased admixture dominated with more San women than men contributing to newcomers. Southern San closer genetically to Oakhurst than northern San due to latitude-correlated FST. Oakhurst San genetic diversity matches other African hunter-gatherers and exceeds European Stone Age foragers. qpWave confirms genetic indistinguishability across Oakhurst chronological groups until 1,300 cal BP. Non-San ancestry postdates archaeological pastoralism by up to 2,000 years. Some southern San individuals today preserve pure Pleistocene-derived ancestry. European admixture hit southern San hardest, increasing their genetic heterogeneity. Northern San show lower non-African admixture variability than southern groups.