GPS data indicate 30-40 mm yr(-1) present-day crustal shortening across the Andes, whereas geological evidence shows crustal shortening concentrated in the sub-Andean thrust belt at a much lower rate (<15 mm yr(-1)). We reconcile the discrepancy between the geodetic and the geological crustal shortening using geodynamic modeling that includes timescale-dependent crustal deformation. The GPS velocities reflect the instantaneous deformation in the Andes that includes both permanent deformation and elastic deformation that will be recovered during future earthquakes, whereas the lower geological rates reflect only the permanent deformation. The three-dimensional viscoelastic model predicts nearly uniform short-term velocity gradients across the Andes, similar to the GPS results, and concentrated long-term crustal shortening in the sub-Andean thrust zone, consistent with geological observations.