A supply chain (SC) is a network of independent manufacturing and logistics companies that perform the critical functions in the order fulfillment process. This paper proposes an effective and modular model to describe material, financial and information flow of SCs at the operational level based on first-order hybrid Petri nets (PNs), i.e., PNs that make use of first-order fluid approximation. The proposed formalism enables the SC designer to choose suitable production rates of facilities in order to optimize the chosen objective function. The optimal mode of operation is performed based on the state knowledge of the obtained linear discrete-time, time-varying state variable model in order to react to unpredictable events such as the blocking of a supply or an accident in a transportation facility. A case study is modeled in the proposed framework and is simulated under three different closed-loop control strategies.