An unusually short glaciation interrupted the warm Pliocene around 3.3 Ma (Marine Isotope Stage (MIS) M2). Different hypotheses exist to explain why this glaciation event was so pronounced, and why the global climate system returned to warm Pliocene conditions relatively quickly afterwards. One of these proposed mechanisms is a reduced equator-to-pole heat transfer, in response to a tectonically reduced Indonesian Throughflow (ITF). The ITF is a critical part of the global thermohaline ocean circulation, transporting heat from the Indo-Pacific Warm Pool to the Indian Ocean. When ITF connectivity is reduced, the water and heat supply for the Leeuwin Current, flowing poleward along Australia's west coast, is also diminished. To assess the possible relationship between mid-Pliocene glaciations and latitudinal heat transport through the Indonesian Throughflow, we constructed a multi-proxy orbital-scale record for the 3.7–2.8 Ma interval from International Ocean Discovery Program (IODP) Site U1463, off northwest Australia. The comparison of the Site U1463 record with paleoclimate records from nearby Site 763 and West Pacific Warm Pool Site 806 allows for a detailed regional reconstruction of Pliocene paleoceanography and thus for testing the proposed hypothesis.An astronomically-paced decrease in potassium content characterizes the late Pliocene interval of U1463. This record documents the increasing aridity of northwest Australia, periodically alleviated by reinforced summer monsoon precipitation under summer insolation maxima. The δ18O record of the planktonic foraminifer Globigerinoides sacculifer correlates exceptionally well with the sea surface temperature (SST) record from Site 806 in the West Pacific Warm Pool, even during MIS M2. Hence, Site U1463 preserves an uninterrupted ITF signal even during Pliocene glaciations. However, the U1463 δ18OG.sacculifer record exhibits a 0.5‰ offset with the nearby Site 763A record around MIS M2. This implies that Site 763A, about 500 km west of U1463, more closely tracks Indian Ocean SST records across MIS M2. The U1463 data reveal that heat-transport through the Indonesian Throughflow did not shut down completely during MIS M2, but rather its intensity decreased prior to and during MIS M2, causing Site 763A to temporarily reflect an Indian Ocean, rather than an ITF signal. We conclude that ITF variability significantly influenced latitudinal heat transport by means of the Leeuwin Current and hence contributed to the relative intensity of MIS M2. We propose the ITF valve between the Pacific and Indian Ocean as a positive feedback mechanism, in which an initial sea level lowering reduces ITF heat transport, in turn amplifying global cooling by advancing the thermal isolation of Antarctica.