<jats:title>Abstract</jats:title><jats:p>Crossing a key atmospheric CO<jats:sub>2</jats:sub> threshold triggered a fundamental global climate reorganisation ~34 million years ago (Ma) establishing permanent Antarctic ice sheets. Curiously, a more dramatic CO<jats:sub>2</jats:sub> decline (~800–400 ppm by the Early Oligocene(~27 Ma)), postdates initial ice sheet expansion but the mechanisms driving this later, rapid drop in atmospheric carbon during the early Oligocene remains elusive and controversial. Here we use marine seismic reflection and borehole data to reveal an unprecedented accumulation of early Oligocene strata (up to 2.2 km thick over 1500 × 500 km) with a major biogenic component in the Australian Southern Ocean. High-resolution ocean simulations demonstrate that a tectonically-driven, one-off reorganisation of ocean currents, caused a unique period where current instability coincided with high nutrient input from the Antarctic continent. This unrepeated and short-lived environment favoured extreme bioproductivity and enhanced sediment burial. The size and rapid accumulation of this sediment package potentially holds ~1.067 × 10<jats:sup>15</jats:sup> kg of the ‘missing carbon’ sequestered during the decline from an Eocene high CO<jats:sub>2</jats:sub>-world to a mid-Oligocene medium CO<jats:sub>2</jats:sub>-world, highlighting the exceptional role of the Southern Ocean in modulating long-term climate.</jats:p>