Philip Zinckernagel gave the Fire the lead in the 37th minute, but New York City scored the next three goals to take a 3-1 victory Saturday night at Soldier Field.
Nicolas Fernandez scored in the 40th minute, Alonso Martinez in the 57th and Seymour Garfield-Reid in the third minute of stoppage time to seal the deal.
Zinckernagel scored his 13th goal in his first season in MLS. Brian Gutierrez earned his fifth assist on the score.
Seventeen-year-old Garfield-Reid scored his first goal in his seventh appearance. He subbed in for Martinez in the 90th minute.
Matt Freese finished with two saves for NYC (14-9-5), and Chris Brady had two for the Fire (12-11-6).
The Fire had won two of their last three to move into the ninth and final playoff spot in the MLS Eastern Conference, two points behind NYC. The result moved NYC into seventh, with Miami in eighth, four points ahead of the Fire.