A method for generating an application-aware virtual topology (AAVT) routing table for a network device among network devices connected via a wide area network is provided. The method is executed by a network controller connected to the network and includes: receiving, from the network devices, path information of the network devices; generating, using the path information, an underlay graph specifying a path topology of the network device; generating, based on the path topology specified in the underlay graph, the AAVT routing table for the network device where the AAVT routing table includes a set of paths; and transmitting, in response to generating the AAVT routing table, the AAVT routing table to the network device to cause the network device to program the set of paths.