The integration of Distributed Energy Resources (DERs) introduces non-conventional two-way power flows which cannot be captured well by traditional model-based techniques. This brings great challenges to accurately localize faults and initiate correct actions of the protection system. In this paper, we propose a data-driven fault localization strategy based on multi-level system regionalization and probabilistic fault detections on all the sub-regions. The strategy combines the Support Vector Data Description (SVDD) and the Kernel Density Estimation (KDE) to provide the confidence level of fault detections in each sub-region by the p values, and then accurately localize the fault by comparing the p values. Our experiments show that the proposed data-driven fault localization can greatly increase the accuracy of fault localization for distribution systems with high integration of DERs.