Deep incised glacial valleys surrounded by high peaks form the modern topography of the Southern Patagonian Andes. Two Miocene plutonic complexes in the Andean retroarc, the cores of the Fitz Roy (49°S) and Torres del Paine (51°S) massifs, were emplaced at 16.7±0.3 Ma and 12.5±0.1 Ma, respectively. Subduction of ocean ridge segments initiated at 54°S, generating northward opening of an asthenospheric window with associated mantle upwelling and orogenic shortening since 16 Ma. Subsequently, the onset of major glaciations at 7 Ma caused drastic changes in the regional topographic evolution. To constrain the respective contributions of tectonic convergence, mantle upwelling and fluvio-glacial erosion to rock exhumation, we present inverse thermal modeling of a new dataset of zircon and apatite (U-Th)/He from the two massifs, complemented by apatite 4He/3He data for Torres del Paine. Our results show rapid rock exhumation recorded in the Fitz Roy massif between 10.5 and 9 Ma, which we ascribe to mantle upwelling and/or crustal shortening due to ridge subduction at 49°S. Both massifs record a pulse of rock exhumation between 6.5 and 4.5 Ma, which we interpret as the result of the onset of Patagonian glaciations. After a period of erosional quiescence during the Miocene/Pliocene transition, increased rock exhumation since 3-2 Ma to present day is interpreted as the result of alpine glacial valley carving promoted by reinforced glacial-interglacial cycles. This study demonstrates that along-strike thermochronological studies provide us with the means to assess the spatio-temporal variations in tectonic, mantle, and surface processes forcing on rock exhumation.