The Eocene-Oligocene transition (EOT) marked the initiation of large-scale Antarctic glaciation. This fundamental change in Cenozoic climate state is recorded in deep-sea sediments by a rapid benthic foraminiferal δ18O increase and appearance of ice-rafted debris in the Southern Ocean. However, we know little about the magnitude of cooling associated with the EOT in shallow water environments, particularly at mid- to high-latitudes. Here we present new paleomagnetic and stratigraphic records of the C13r/C13n magnetochron boundary and the EOT in the clay-rich Blanche Point Formation (BPF), South Australia. The BPF was deposited in a shallow shelf setting (water depths of <100 m) at a paleolatitude of ~51 °S. We present high-resolution δ18O, δ13C, and Mg/Ca records of environmental change from well-preserved benthic foraminifera of latest Eocene age at this site. A marked, negative δ13C excursion occurs immediately before a δ18O increase, which may be a globally representative signal. A ~2 °C cooling of shallow shelf seawater is evident from benthic foraminiferal Mg/Ca across EOT Step 1, the first step in the two-step benthic foraminiferal δ18O increase across the EOT. This cooling signal is both sufficient to account fully for the δ18O increase in our data and is of similar amplitude to that documented in published records for shallow shelf and the upper water column in open ocean settings, which suggests no obvious polar amplification of this cooling signal. Our results strengthen the evidence base for attributing EOT Step 1 to global cooling with little contribution from ice volume growth and contradict the mechanism suggested to explain the inferred northward migration of the intertropical convergence zone in the contemporaneous equatorial Pacific Ocean.