In the passive margin of southeast Australia, a mosaic of tectonic structures of the Otway Basin records the protracted Cretaceous to Eocene break‐up evolution of Australia and Antarctica. Here, we use an innovative approach that combines Euler deconvolution and DBSCAN clustering of global magnetic data and drill‐hole‐constrained interpretations of deep 2D seismic traverse to image deep‐rooted, pre‐rifting basement crustal structures now covered by passive margin basins. The method is used to identify the complex network of Early Paleozoic faults that were reactivated and transformed into major basing‐bounding listric faults during Cretaceous rifting. Major faults identified include the Bambra, Avoca, Yarramyljup, and Moyston faults. The Yarramyljup and Moyston faults segmented the Cretaceous Otway Basin, demonstrating how basement lithospheric heterogeneities can influence basin development. Our analysis also redefines the northwest margin of the Proterozoic VanDieland microcontinent. This microcontinent acted as a rigid crustal block during the Cretaceous extension and influenced the geometries of the passive margin basin depocenters. These insights transform our understanding of the crustal architecture and structural inheritance in the tectonic evolution of southeast Australia and establish a template for imagining deep crustal structures elsewhere. Plain Language Summary: We introduced a new method to investigate deep geology in the southeast Australian margin, a region that underwent several phases of extension during its break‐up with Antarctica about 100 million years ago. We used geophysical methods and machine learning to determine the depth of geological features, showing how the network of faults under the overlying Otway Basin influenced this breakup. These findings enhance our understanding of the region's past and offer a new approach to investigating buried crustal structures in similar geologic environments. Key Points: DBSCAN‐clustered Euler depth solutions help infer deep structures obscured by near‐surface geological features in geophysical dataThe new basement network shows the Bambra Fault truncates the N‐S Avoca Fault but not the NNW‐SSE or NNE Yarramyljup and Moyston FaultsSteep‐dipping faults are reactivated into major listric faults, segmenting extensional faults during continental break‐up [ABSTRACT FROM AUTHOR]

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