The standard hot-plug controller (SHPC) specification may be used to generate PCI messages in a distributed switch to disconnect and/or connect virtual hierarchies of an endpoint from hosts that are connected based on multi-root input/output virtualization (MR-IOV). A management controller may instruct a SHPC to generate a PCI packet that specifies a particular virtual hierarchy to disconnect from a particular host. An upstream port connected to the host and the SHPC receives the PCI packet and uses a header that identifies the virtual endpoint in the packet to index into a routing table to identify a downstream port in the distributed switch that is connected to the endpoint. Once the PCI packet traverses the switch and arrives at the downstream port, the downstream port changes routing logic which logically disconnects the host from the specified virtual hierarchy.