The lifetime and spatial distributions of accumulation-mode aerosols in a size range of approximately 0.05-1 μm, and thus their global and regional climate impacts, are primarily constrained by their removal via cloud and precipitation (wet removal). However, the microphysical process that predominantly controls the removal efficiency remains unidentified because of observational difficulties. Here, we demonstrate that the activation of aerosols to cloud droplets (nucleation scavenging) predominantly controls the wet removal efficiency of accumulation-mode aerosols, using water-insoluble black carbon as an observable particle tracer during the removal process. From simultaneous ground-based observations of black carbon in air (prior to removal) and in rainwater (after removal) in Tokyo, Japan, we found that the wet removal efficiency depends strongly on particle size, and the size dependence can be explained quantitatively by the observed size-dependent cloud-nucleating ability. Furthermore, our observational method provides an estimate of the effective supersaturation of water vapour in precipitating cloud clusters, a key parameter controlling nucleation scavenging. These novel data firmly indicate the importance of quantitative numerical simulations of the nucleation scavenging process to improve the model's ability to predict the atmospheric aerosol burden and the resultant climate forcings, and enable a new validation of such simulations.