The ocean is the main source of thermal inertia in the climate system. Ocean heat uptake during recent decades has been quantified using ocean temperature measurements. However, these estimates all use the same imperfect ocean dataset and share additional uncertainty due to sparse coverage, especially before 2007. Here, we provide an independent estimate by using measurements of atmospheric oxygen (O-2) and carbon dioxide (CO2) - levels of which increase as the ocean warms and releases gases - as a whole ocean thermometer. We show that the ocean gained 1.29 +/- 0.79 x 10(22) Joules of heat per year between 1991 and 2016, equivalent to a planetary energy imbalance of 0.80 +/- 0.49W watts per square metre of Earth's surface. We also find that the ocean-warming effect that led to the outgassing of O-2 and CO2 can be isolated from the direct effects of anthropogenic emissions and CO2 sinks. Our result - which relies on high-precision O-2 atmospheric measurements dating back to 1991 - leverages an integrative Earth system approach and provides much needed independent confirmation of heat uptake estimated from ocean data.