The Paraná Basin, Brazil and the Chaco-Paraná Basin, Uruguay both contain sedimentary records that are critical to reconstructing late Paleozoic ice centers in central Gondwana. The orientations of subglacial landforms and glaciotectonic structures suggest that late Paleozoic glacial deposits in the eastern Chaco-Paraná Basin and the southernmost Paraná Basin are genetically related, as they were likely glaciated by the same ice center. However, the location and extent of the ice center responsible for depositing these sediments are unclear. Furthermore, changes in sediment dispersal patterns between glacial, inter-glacial, and post-glacial intervals are not understood for this region of Gondwana. Therefore, this study utilized U–Pb detrital zircon geochronology to assess the provenance of glacial and post-glacial sediments from the eastern Chaco-Paraná Basin (San Gregorio, Cerro Pelado, Tres Islas Formations) and the southernmost Paraná Basin (Itararé Group). Results show dominant age peaks at ~520–555 Ma, ~625 Ma, 750–780 Ma, and 900–1000 Ma in all samples from the eastern Chaco-Paraná Basin. These zircons are interpreted to have been derived from sources in the Cuchilla Dionisio Terrane and Punta del Este Terrane in southeastern Uruguay, and possibly the Namaqua Belt in southern Namibia. Another important source was likely Devonian sedimentary rocks of the Durazno Group in central/eastern Uruguay. Meanwhile, a sample of the glaciogenic Itararé Group from the southernmost Paraná Basin contains a different detrital zircon signature with peaks at ~580 Ma, ~780 Ma, ~2110 Ma, and ~2500 Ma that closely resembles underlying sedimentary and meta-sedimentary rocks of the Precambrian/Cambrian Camaquã Basin. Detrital zircon ages in the glacial and post-glacial sediments indicate that local sources were dominant. In contrast, zircon ages from relatively ice-distal glaciomarine intervals in the Chaco-Paraná Basin reflect more distal sources to the east and southeast, which indicates a larger drainage catchment opened when glaciers retreated and/or the zone of maximum subglacial erosion shifted. Although most zircon ages in the Chaco-Paraná Basin can be attributed to Uruguayan sources, results support the hypothesis that glaciers emanated from southern Namibia and southeast Uruguay into the Chaco-Paraná Basin. From there, ice flowed northwest into the Paraná Basin and then receded back towards Africa as the paleoclimate warmed. The detrital zircon inventory in our study region is distinct from the eastern Paraná Basin, suggesting at least two unique African source regions for glaciers that deposited sediments in the Paraná and Chaco-Paraná Basins.