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Cyber-Physical Systems (CPSs) are increasingly important in critical areas of our society such as intelligent power grids, next generation mobile devices, and smart buildings. CPS operation has characteristics including considerable heterogeneity, variable dynamics, and high complexity. These systems have also scarce resources in order to satisfy their entire load demand, which can be divided into data processing and service execution. These new characteristics of CPSs need to be managed with novel strategies to ensure their resilient operation. Towards this goal, we propose an SDN-based solution enhanced by distributed Network Function Virtualization (NFV) modules located at the top-most level of our solution architecture. These NFV agents will take orchestrated management decisions among themselves to ensure a resilient CPS configuration against threats, and an optimum operation of the CPS. For this, we study and compare two distinct incentive mechanisms to enforce cooperation among NFVs. Thus, we aim to offer novel perspectives into the management of resilient CPSs, embedding IoT devices, modeled by Game Theory (GT), using the latest software and virtualization platforms.