We combine lidar temperature observations onboard a research aircraft with numerical simulations in the framework of the SOUTHTRAC (Southern Hemisphere Transport, Dynamics, and Chemistry) Campaign. Deep propagation of gravity waves (GW) from the troposphere to the lower mesosphere is studied above the Southern Andes during two flights in September 2019. We use the Weather Research and Forecasting (WRF) model with a configuration for the simulations that has been validated in a previous study of this campaign. Strong orographic GW were detected during both flights, that were conceived for different latitudes. The observational and numerical data reveal the presence of significant GW attenuation, breaking and secondary wave generation above the stratopause due to the development of convective and dynamic instability as well as conditions for wave evanescence. The GW generated by topography were not able to alter the stable structure of the stratosphere, but the scenario was quite different in the lower mesosphere. The disturbed zones in that layer were produced by the combined effect on lapse rate of the background temperature variation and the perturbations associated with GW, which together may induce large vertical gradients. As a consequence, areas of reduced stability (with low or even negative buoyancy parameter) emerge above the stratopause. The existence of these GW self-induced attenuation layers in the mesosphere where temperature perturbations produce large negative gradients may lead to an amplitude growth control mechanism for the upward propagating waves.