Recent advances in causality analysis have enabled investigators to trace multi-stage attacks using provenance graphs. Based on system-layer audit logs (e.g., syscalls), these approaches omit vital sources of application context (e.g., email addresses, HTTP response codes) that can be found in higher layers of the system. Although such information is often essential to understanding attack behaviors, it is difficult to incorporate this evidence into causal analysis engines because of the semantic gap that exists between system layers. To address that shortcoming, we propose the notion of universal provenance, which encodes all forensically relevant causal dependencies regardless of their layer of origin. To transparently realize that vision on commodity systems, we present OmegaLog, a provenance tracker that bridges the semantic gap between system and application logging contexts. OmegaLog analyzes program binaries to identify and model application-layer logging behaviors, enabling accurate reconciliation of application events with system-layer accesses. OmegaLog then intercepts applications’ runtime logging activities and grafts those events onto the system-layer provenance graph, allowing investigators to reason more precisely about the nature of attacks. We demonstrate that our system is widely applicable to existing software projects and can transparently facilitate execution partitioning of provenance graphs without any training or developer intervention. Evaluation on real-world attack scenarios shows that our technique generates concise provenance graphs with rich semantic information relative to the state-of-the-art, with an average runtime overhead of 4%.