A turnover of the pinniped fauna took place in the Southern Hemisphere during the Pliocene, based on evidence from South America and South Africa. This resulted in the extinction of early phocids, which were replaced by otariids dispersing from the North Pacific. There is currently a lack of evidence of a similar event from Australia, with the only confirmed phocids from the Miocene–Pliocene boundary and the earliest confirmed otariids from the late Pleistocene. Here, we report a fossil monachine tooth from the Pliocene Whalers Bluff Formation of Portland (Victoria). The tooth represents an extinct monachine seal; it does not resemble either crown lobodontins or miroungins. This is the geologically youngest pre-Holocene occurrence of Phocidae in Australia, and one of the youngest pre-Pleistocene records of phocids in the Southern Hemisphere. It extends the maximum known geochronological range of monachines in the fossil record of Australia to between 6.2 and 2.67 Ma. It is possible that pinniped faunal turnovers in the Southern Hemisphere all occurred during the late Pliocene, with the turnover in Australia occurring sometime after 4.31 Ma. The description of additional Australasian fossil pinnipeds will further constrain this faunal turnover event.