Value chain is identified as the generator of the metabolic rift between nature and society. However, the sustainable value chain can mitigate and reverse this rift. In this paper, firstly, a review of the main digital enablers of Industry 4.0 and the current state of cognitive manufacturing is carried out. Secondly, Cyber-Physical Systems are conceived from the holonic paradigm, as an organizational enabler for the whole of enablers. Thirdly, the bijective relationship between holonic paradigm and container-based technology is analyzed. This technology allows mapping the physical and virtual holon as an intelligent agent embodied at the edge, fog and cloud level, with physical and virtual part. Finally, the proposed holonic system based on the cyber-physical holon is developed through multi-agent systems based on container technology. The proposed system allows to model the metabolism of manufacturing systems, from a cell manufacturing to whole value chain, in order to develop, evolve and improve the sustainable value chain.