Basic toolmaking techniques began to undergo additional change about 40,000 years ago. Small finely worked stone implements known as microliths became more common, while the heavier scrapers and points of the Middle Stone Age appeared less frequently. Archaeologists refer to this technological stage as the Late Stone Age. The numerous collections of stone tools from South African archaeological sites show a great degree of variation through time and across the subcontinent.

The remains of plant foods have been well preserved at such sites as Melkhoutboom Cave, De Hangen, and Diepkloof in the Cape region. Animals were trapped and hunted with spears and arrows on which were mounted well-crafted stone blades. Bands moved with the seasons as they followed game into higher lands in the spring and early summer months, when plant foods could also be found. When available, rock overhangs became shelters; otherwise, windbreaks were built. Shellfish, crayfish, seals, and seabirds were also important sources of food, as were fish caught on lines, with spears, in traps, and possibly with nets.

Dating from this period are numerous engravings on rock surfaces, mostly on the interior plateau, and paintings on the walls of rock shelters in the mountainous regions, such as the Drakensberg and Cederberg ranges. The images were made over a period of at least 25,000 years. Although scholars originally saw the South African rock art as the work of exotic foreigners such as Minoans or Phoenicians or as the product of primitive minds, they now believe that the paintings were closely associated with the work of medicine men, shamans who were involved in the well-being of the band and often worked in a state of trance. Specific representations include depictions of trance dances, metaphors for trance such as death and flight, rainmaking, and control of the movement of antelope herds.

Pastoralism and early agriculture

New ways of living came to South Africa about 2,000 years ago. Until that time, human communities had survived by gathering plant foods and by hunting, trapping, and scavenging for meat, but with the introduction of agriculture—arguably the single most important event in world history—people began to make use of domesticated animals and plants. This in turn led to a slow but steady rise in population and to more-complex political and religious organizations, among other things. Crops could be grown and cattle, sheep, and goats herded near permanent villages and towns in the east, where rainfall was adequate. In the more arid west, domestic livestock were kept by nomadic pastoralists, who moved over wide territories with their flocks and herds.

Although the origin of nomadic pastoralism in South Africa is still obscure, linguistic evidence points to northern Botswana as a probable source. The linguistic evidence is supported by finds of sheep bones and pottery from Bambata Cave in southwestern Zimbabwe that have been dated to about 150 bce. Whether new communities moved into South Africa with their flocks and herds or whether established hunter-gatherer bands took up completely new ways of living remains unclear. In any case, the results of archaeological excavations have shown that sheep were being herded fairly extensively by the first few centuries ce in eastern and western parts of the Cape and probably in the northern Cape as well.

While traces of ancient herding camps tend to be extremely rare, one of the best-preserved finds is at Kasteelberg, on the southwest coast near St. Helena Bay. Pastoralists there kept sheep, hunted seals and other wild animals, and gathered shellfish, repeatedly returning to the same site for some 1,500 years. Such communities were directly ancestral to the Khoekhoe (also spelled Khoikhoi) herders who encountered European settlers at the Cape of Good Hope in the mid-17th century.

The archaeological traces of farmers in the eastern regions of South Africa are more substantial. The earliest sites date to the 3rd century ce, although farming was probably already well established by this time. Scatters of potsherds with distinctive incised decoration mark early village locations in Mpumalanga and parts of KwaZulu-Natal.