Maurice Edu headed a long cross in front of the goal and Sapong found the back of the net in the 86th minute to ensure the spoils were shared at Yankee Stadium.
Philadelphia (1-3-3) beat NYC FC (1-2-3) 2-1 in stoppage time five days ago to record their lone victory of the season.
Mehdi Ballouchy had put New York ahead in the 57th minute when he curled a shot in the net from just inside the area.
City goalkeeper Josh Saunders saved from Sheannon Williams and Sebastien Le Toux as Union pushed for an equaliser, which they eventually got it with time running out to earn a hard-fought point.
Khiry Shelton, the second overall draft pick in the 2015 MLS SuperDraft, made his first start for New York.
Watch the MLS this weekend on Sky Sports 5 HD. New York Red Bulls face San Jose Earthquakes at midnight, while Philadelphia Union are back in action against New England Revolution at 10pm BST on Sunday.