A domain partitioning system for a multi-node computer system is disclosed. An external server manager is coupled to a domain configuration unit by a dedicated sideband channel. The server manager has write privileges to the domain configuration unit that allows the server manager to control the domain partitioning and the routing tables. None of the domains of the computer system are permitted write access to the domain configuration unit. In one embodiment, the domain configuration unit is a set of domain partition registers and routing table registers coupled to a system interconnect.