South America was isolated during most of the Cenozoic, and it was home to an endemic fauna. The South American Native Ungulates (SANUs) exhibited high taxonomical, morphological, and ecological diversity and were widely distributed on the continent. However, most SANU fossil records come from high latitudes. This sampling bias challenges the study of their diversity dynamics and biogeography during important tectonic and biotic events, such as the Great American Biotic Interchange, the faunal exchange between North and South America after the formation of the Isthmus of Panama. We describe new SANU remains from the Neogene of the Cocinetas (northern Colombia) and Falcón (northwestern Venezuela) Basins. In the Cocinetas Basin, the middle Miocene fauna of the Castilletes Formation includes Hilarcotherium miyou sp. nov. (Astrapotheriidae), cf. Huilatherium (Leontiniidae), and Lambdaconus cf. L. colombianus (Proterotheriidae). The late Pliocene fauna of the Ware Formation includes a Toxodontinae indet. and the putative oldest record of Camelidae in South America. In the Falcón Basin, the Pliocene/Pleistocene faunas of the Codore and San Gregorio Formations include Falcontoxodon aguilerai gen. et sp. nov. and Proterotheriidae indet. We provide a phylogenetic analysis for Astrapotheriidae and Toxodontidae. The new data document a low-latitude provinciality within some SANU clades (e.g., Astrapotheriidae, Leontiniidae) during the middle Miocene. This contrasts with the wide latitudinal distribution of clades of other mammals recorded in the fauna, including the sparassodont Lycopsis padillai, the sloth Hyperleptus?, and the proterotheriid Lambdaconus cf. L. colombianus. The Pliocene/Pleistocene tropical faunas from northern South America are characterized by the predominance of native taxa despite their proximity to the Isthmus of Panama (fully emerged by that time). Only one North American ungulate herbivore immigrant is present, a cf. Camelidae indet. The Pliocene and early Pleistocene faunas suggest that environmental changes and biotic interactions affected the diversity dynamics and biogeographic patterns of SANUs during the Great American Biotic Interchange.