Hedges scored on a set-piece off a Michel free kick and the Brazilian midfielder later added an insurance goal for FCD (11-11-11), which won in head Coach Schellas Hyndman's final home match.
The Sounders (15-12-6), meanwhile, blew a chance to wrap up a Western Conference playoff berth with their team-record fourth straight defeat.
Seattle has struggled since winning eight times in nine games during the middle of the season.
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