Nearly a century of paleontological excavation and analysis from the cave deposits of the Cradle of Humankind UNESCO World Heritage Site in northeastern South Africa underlies much of our understanding of the evolutionary history of hominins, other primates and other mammal lineages in the late Pliocene and early Pleistocene of Africa. As one of few designated fossil repositories, the Plio-Pleistocene Palaeontology Section of the Ditsong National Museum of Natural History (DNMNH; the former Transvaal Museum) curates much of the mammalian faunas recovered from the fossil-rich deposits of major South African hominin-bearing localities, including the holotype and paratype specimens of many primate, carnivore, and other mammal species (Orders Primates, Carnivora, Artiodactyla, Eulipotyphla, Hyracoidea, Lagomorpha, Perissodactyla, and Proboscidea). Here we describe an open-access digital archive of high-resolution, full-color three-dimensional (3D) surface meshes of all 89 non-hominin holotype, paratype and significant mammalian specimens curated in the Plio-Pleistocene Section vault. Surface meshes were generated using a commercial surface scanner (Artec Spider, Artec Group, Luxembourg), are provided in formats that can be opened in both open-source and commercial software, and can be readily downloaded either via an online data repository (MorphoSource) or via direct request from the DNMNH. In addition to providing surface meshes for each specimen, we also provide tomographic data (both computerized tomography [CT] and microfocus [microCT]) for a subset of these fossil specimens. This archive of the DNMNH Plio-Pleistocene collections represents the first research-quality 3D datasets of African mammal fossils to be made openly available. This simultaneously provides the paleontological community with essential baseline information (e.g., updated listing and 3D record of specimens in their current state of preservation) and serves as a single resource of high-resolution digital data that improves collections accessibility, reduces unnecessary duplication of efforts by researchers, and encourages ongoing imaging-based paleobiological research across a range of South African non-hominin fossil faunas. Because the types, paratypes, and key specimens include globally-distributed mammal taxa, this digital archive not only provides 3D morphological data on taxa fundamental to Neogene and Quaternary South African palaeontology, but also lineages critical to research on African, other Old World, and New World paleocommunities. With such a broader impact of the DNMNH 3D data, we hope that establishing open access to this digital archive will encourage other researchers and institutions to provide similar resources that increase accessibility to paleontological collections and support advanced paleobiological analyses.