In the late twentieth century, the sub-thermocline waters of the southern tropical and subtropical Indian Ocean experienced a sharp cooling. This cooling has been previously attributed to an anthropogenic aerosol-induced strengthening of the global ocean conveyor, which transfers heat from the subtropical gyre latitudes toward the North Atlantic. From the mid-1990s the sub-thermocline southern Indian Ocean experienced a rapid temperature trend reversal. Here we show, using climate models from phase 5 of the Coupled Model Intercomparison Project, that the late twentieth century sub-thermocline cooling of the southern Indian Ocean was primarily driven by increasing anthropogenic aerosols and greenhouse gases. The models simulate a slow-down in the sub-thermocline cooling followed by a rapid warming towards the mid twenty-first century. The simulated evolution of the Indian Ocean temperature trend is linked with the peak in aerosols and their subsequent decline in the twenty-first century, reinforcing the hypothesis that aerosols influence ocean circulation trends.