Seattle Sounders FC defeated defending-champion D.C. United 2–1 in the final at RFK Stadium in Washington, D.C. Both clubs had started in the MLS qualification tourney, and ended up playing 6 matches each.
As in the previous tournament, forty teams qualified to the tournament. The qualifying process for MLS took the form of an eight-team play-off tournament. The top six finishers, regardless of conference, in 2008 were given six of the berths into the Third Round. The eight remaining U.S.-based clubs competed for the final two berths via a playoff.
Continuing the format of recent seasons, no qualification process was needed for USL-1 and USL-2 as each level has exactly eight U.S.-based clubs for the 2009 season. The PDL announced that four selected early season games will again double as qualifying matches, as they had in recent years. Each division received a berth, since there are eight divisions instead of the ten that existed in 2008. The qualifying process for the USASA took the form of four regional tournaments, with the two finalists in each region being awarded berths.