To investigate the lithospheric seismic structure of southern South America beneath the Paraná, Chaco-Paraná, and Pantanal basins, we measure two distinct sets of dispersion curves of Rayleigh waves: the first corresponds to 25,986 phase velocity dispersion curves in the period range 5–50 s, extracted from cross-correlation of the ambient noise between pairs of stations and thus sensitive mainly to crustal structure; the second set is derived from group velocities extracted from earthquake recordings, resulting in 33,888 dispersion curves with periods ranging from 8 to 200 s, allowing us to probe deeper Earth structure. From these data sets, we derive two independent S-wave velocity models following a two-step inversion procedure, resulting in a crustal and a lithospheric mantle model with depths extending up to 50 and 200 km, respectively. Features imaged in our crustal model include low velocity anomalies in agreement with the surface position of the major sedimentary basins and high velocity anomalies within fold-thrust provinces and the basement of the Pantanal basin. In the uppermost mantle, we identify high velocities in the region of the Paraná basin, São Francisco and Amazonian cratons, and Luiz Alves block, and a low velocity feature beneath the Pantanal basin, which suggests a potentially thinner lithosphere under the basin. We also illuminate a strong velocity gradient boundary between the eastern border of the Pantanal basin with the Paraná basin, from crustal to lithospheric mantle depths, which seems to delineate the western and southern borders of the Paraná basin, coinciding with the Western Paraná Suture. Additionally, we construct a Moho depth proxy map for the study area, which has an overall good agreement with previous results, except for a thicker crust beneath the southern Chaco-Paraná basin. This area, together with a thicker crust counterpart in the Paraná basin, has a remarkable correlation with the position of a volcanic layer related to the Paraná Magmatic Province, which leads us to suggest that magmatic processes played an important role in the south Chaco-Paraná basin as well.