Graham Zusi also scored for Kansas City (17-10-7), which will claim the Supporters Shield for the best record in the MLS if New York loses or draws Sunday against Chicago. Philadelphia was eliminated from playoff contentions with the loss and finished the season 12-12-10.
Zusi opened the scoring in the 47th minute. Jack McInerney scored his team-best 12th goal to tie it for Philadelphia in the 88th minute.
Philadelphia lost its final two games and missed the playoffs for the third time in four seasons. The Union played without midfielder and captain Brian Carroll because of yellow card accumulation.