Advanced cyber threats (e.g., Fileless Malware and Advanced Persistent Threat (APT)) have driven the adoption of provenance-based security solutions. These solutions employ Machine Learning (ML) models for behavioral modeling and critical security tasks such as malware and anomaly detection. However, the opacity of ML-based security models limits their broader adoption, as the lack of transparency in their decision-making processes restricts explainability and verifiability. We tailored our solution towards Graph Neural Network (GNN)-based security solutions since recent studies employ GNNs to comprehensively digest system provenance graphs for security-critical tasks. To enhance the explainability of GNN-based security models, we introduce PROVEXPLAINER, a framework offering instance-level security-aware explanations using an interpretable surrogate model. PROVEXPLAINER's interpretable feature space consists of discriminant subgraph patterns and graph structural features, which can be directly mapped to the system provenance problem space, making the explanations human interpretable. We show how PROVEXPLAINER synergizes with current state-of-the-art (SOTA) GNN explainers to deliver domain and instance-specific explanations. We measure the explanation quality using the Fidelity+/Fidelity- metric as used by traditional GNN explanation literature, we incorporate the precision/recall metric, where we consider the accuracy of the explanation against the ground truth, and we designed a human actionability metric based on graph traversal distance. On real-world Fileless and APT datasets, PROVEXPLAINER achieves up to 29%/27%/25%/1.4x higher Fidelity+, precision, recall, and actionability (where higher values are better), and 12% lower Fidelity- (where lower values are better) when compared against SOTA GNN explainers.