Just five days after beating City 2-1 in Philadelphia thanks to a stoppage-time strike from Vincent Nogueira, the Union secured a 1-1 draw in New York when Sapong equalised with four minutes remaining.
It completed a strong week in MLS for the Union, who had started Saturday's first match of the double-header with just two points from five games.
New York had not won in three matches but looked set to pick up three points after Mehdi Ballouchy curled his shot past Union goalkeeper John McCarthy in the 57th minute - the Moroccan midfielder's first goal in MLS since April 2012 when he was playing for City's crosstown rivals New York Red Bulls.
But Sapong, who joined Philadelphia from Sporting Kansas City at the end of last season, levelled the match in the 86th minute at Yankee Stadium, acrobatically volleying into the net from Maurice Edu's knockdown.
The draw dragged Union level with sixth-placed City on six points, although the latter remain just ahead in the Eastern Conference standings due to fewer games played.
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