In its final game of the regular season, Kansas City needed a win or tie to wrap up first place in the conference.
Sapong assisted on a goal by Jacob Peterson in the 40th minute that put Kansas City in front, but Philadelphia tied it early in the second half when Antoine Hoppenot scored for the Union.
The Philadelphia goal was a rare one against Kansas City, which finishes the regular season having given up a league-low 27. Seattle has allowed the second fewest number of goals at 32 with one game to play.
Sapong's winning goal came from the right side of the penalty area off a pass from Kei Kamara.
Kansas City completed the regular campaign with an 18-7-9 record. Philadelphia, which will miss the playoffs, has a 10-17-6 mark with one game remaining.