Observational and atmospheric inversion studies find that the strength of the Southern Ocean carbon dioxide (CO2) sink is not increasing, despite rising atmospheric CO2. However, this is yet to be captured by contemporary coupled-climate-carbon-models used to predict future climate. We show that by accounting for stratospheric ozone depletion in a coupled-climate-carbon-model, the ventilation of carbon rich deep water is enhanced through stronger winds, increasing surface water CO2 at a rate in good agreement with observed trends. We find that Southern Ocean uptake is reduced by 2.47 PgC (1987–2004) and is consistent with atmospheric inversion studies. The enhanced ventilation also accelerates ocean acidification, despite lesser Southern Ocean CO2 uptake. Our results link two important anthropogenic changes: stratospheric ozone depletion and greenhouse gas increases; and suggest that studies of future climate that neglect stratospheric ozone depletion likely overestimate regional and global oceanic CO2 uptake and underestimate the impact of ocean acidification.