A physical networking/virtual infrastructure management integration system includes a physical networking infrastructure management system providing physical networking infrastructure management subsystems, a virtual infrastructure management system providing virtual infrastructure management subsystems, and a network integration system. The network integration system identifies at least one affiliation between service endpoints provided by the physical networking infrastructure management subsystems and the virtual infrastructure management subsystems, and generates an affiliation graph that identifies each of the service endpoints and each affiliation between pairs of the service endpoints. The network integration system then converts the affiliation graph to a bipartite graph that includes a controller group including a first subset of the service endpoints and a controlled group including a second subset of the service endpoints, and launches a respective service container for each of the first subset of the service endpoints in the controller group.