Federated cyber-physical systems (CPSs) present unique security challenges due to their distributed nature and the need for secure communication between components from different administrative domains. Distributed ledger technology (DLT) offers a promising approach to implementing a resilient authentication and authorization mechanism and an immutable record of CPS identities and transactions in federated environments. However, using Distributed Ledger (DL) within a CPS raises some important questions regarding scalability, throughput, latency, and potential bottlenecks, which require effective modeling of DL performance. This paper proposes a novel approach to modeling distributed ledgers using Colored Timed Petri Nets (CPNs). We focus on the performance modeling of Hyperledger Fabric (HLF), a permissioned distributed ledger technology which provides a backbone for a Lightweight Authentication and Authorization Framework for Federated IoT (LAAFFI), a novel framework for secure communication between CPS devices. We implement our model using CPN Tools, a widely adopted CPN modeling software that provides advanced simulation, analysis, and performance monitoring features. Our model offers a robust framework for studying distributed ledger systems' synchronization, throughput, and response time. It supports flexibility in modeling transaction validation and consensus algorithms, which provides an opportunity for adapting the model to future changes in HLF and modeling other DLs. We successfully validate our CPN model by comparing simulation results with experimental measurements obtained from a LAAFFI prototype.