Employing surface mapping of syntectonic sediments, interpretation of industry reflection-seismic profiles, gravity data, and isotopic age dating, we reconstruct the tectonic evolution of the southern Altiplano (∼20–22°S) between the cordilleras defining its margins. The southern Altiplano crust was deformed between the late Oligocene and the late Miocene with two main shortening stages in the Oligocene (33–27 Ma) and middle/late Miocene (19–8 Ma) that succeeded Eocene onset of shortening at the protoplateau margins. Shortening rates in the southern Altiplano ranged between 1 and 4.7 mm/yr with maximum rates in the late Miocene. Summing rates for the southern Altiplano and the Eastern Cordillera, we observe an increase from Eocene times to the late Oligocene to some 8 mm/yr, followed by fluctuation around this value during the Miocene prior to shutoff of deformation at 7–8 Ma and transfer of active shortening to the sub-Andean fold and thrust belt. Shortening inverted early Tertiary graben and half graben systems and was partitioned in three fault systems in the western, central, and eastern Altiplano, respectively. The east vergent fault systems of the western and central Altiplano were synchronously active with the west vergent Altiplano west flank fault system. From these data and from section balancing, we infer a kinematically linked western Altiplano thrust belt that accumulated a minimum of 65 km shortening. Evolution of this belt contrasts with the Eastern Cordillera, which reached peak shortening rates (8 mm/yr) in between the above two stages. Hence local shortening rates fluctuated across the plateau superimposed on a general trend of increasing bulk rate with no trend of lateral propagation. This observation is repeated at the shorter length and time scales of individual growth structures that show evidence for periods of enhanced local rates at a timescale of 1–3 Myr. We interpret this irregular pattern of deformation to reflect a plateau-style of shortening related to a self-organized state of a weak crust in the central South American back arc with a fault network that fluctuated around the critical state of mechanical failure. Tuning of this state may have occurred by changes in plate kinematics, during the Paleogene, initially reactivating crustal weak zones and by thermal weakening of the crust with active magmatism mainly in the Neogene stage.