Drought-induced mortality is expected to cause substantial biomass loss in the Amazon basin. However, rainforest responses to prolonged drought are largely unknown. Here, we demonstrate that an Amazonian rainforest plot subjected to more than two decades of large-scale experimental drought reached eco-hydrological stability. After elevated tree mortality during the first 15 years, ecosystem-level structural changes resulted in the remaining trees no longer experiencing drought stress. The loss of the largest trees led to increasing water availability for the remaining trees, stabilizing biomass in the last 7 years of the experiment. Hydraulic variables linked to physiological stress, such as leaf water potential, sap flow and tissue water content, converged to the values observed in a corresponding non-droughted control forest, indicating hydraulic homeostasis. While it prevented drought-induced collapse, eco-hydrological stabilization resulted in a forest with reduced biomass and carbon accumulation in wood. These findings show how tropical rainforests may be resilient to persistent soil drought.