An automated multi-fabric link aggregation system includes leaf switch devices that have leaf switch device downlink ports, that are included in a first network fabric, and that are aggregated to provide a first aggregation fabric. Each leaf switch device generates discovery communications including a first network fabric identifier for the first network fabric, and a first aggregation fabric identifier for the first aggregation fabric. The leaf switch devices then transmit the discovery communications via the leaf switch device downlink ports. I/O modules that have I/O module uplink port are included in a second network fabric and are aggregated to provide a second aggregation fabric. The I/O modules receive the discovery communications via each of the I/O module uplink ports, determine that each received discovery communication includes the first network fabric identifier and the first aggregation fabric identifier and, in response, automatically configure the I/O module uplink ports in a LAG.