Functionally extinct ecosystems, those that have been locally eradicated save for remnant individuals, are unlikely to naturally recover over meaningful human time frames. However, ecosystem restoration provides opportunities to reverse functional extinction by rapidly addressing the physical and/or biological barriers that prevent natural recovery. Here, we assess the restoration progress of a native Flat oyster (Ostrea angasi) reef ecosystem in South Australia that was eradicated from the Australian mainland approximately 100 years ago. In the absence of any reference Flat oyster ecosystems in the region, restoration progress was assessed relative to ecological targets informed by a combination of local rocky reef ecosystems and an interim Flat oyster reference model informed by Australia's sole remaining O. angasi reef, in Tasmania. Two and half a years after the restoration was initiated via the construction of 14 boulder reefs, we observed densities of restored native adult O. angasi (192 ± 19 m−2; mean ± 1 SE) that exceeded oyster densities observed on the sole remaining natural reef. Communities of macroinvertebrates on the reef restoration represented approximately 60% of the biodiversity observed on healthy rocky reef reference systems, while ecological functions (e.g. filter feeding) are demonstrably increasing. The rate of recovery of this benthic ecosystem, from functionally extinct to a restored Flat oyster reef ecosystem within several years, demonstrates the latent resilience of degraded oyster communities and the capacity for effective marine restorations to achieve rapid ecological recoveries.