Davy Arnaud scored in the closing minutes with a penalty kick to account for the Wizards' goal.
Kansas City (9-12-6) would need to win its final three regular-season games and Colorado Rapids would have to lose its last two for the Wizards to reach post-season play.
Nyassi scored in the 66th minute when he knocked home a rebound for his second goal of the season.
Fernandez got his second goal of the season for Seattle (13-9-6) in the 78th minute.
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