NYCFC entered the night winless in six matches, having lost three times and picked up three draws since the club's last win over Torton FC on August 12.
But the side returned to winning ways and secured a postseason spot for the third consecutive year thanks to goals from Alexander Ring and David Villa.
After an uneventful first half, Ring opened the scoring early in the second half, curling home after having been set up with by a clever touch from Villa.
Villa got on the scoresheet four minutes later, getting on the end of a Maxi Moralez cut-back to make it 2-0.
NYCFC sits third in the Eastern Conference and 10 points adrift of Supporters' Shield leader Atlanta United with three matches remaining in the regular season.
Domènec Torrent's club could still finish second in the East and earn a first-round playoff bye, but will need some help to catch up to the New York Red Bulls, who sit six points clear and have a game in hand on City.
For Chicago, Wednesday's loss ended any hopes of reaching the playoffs with the club now mathematically eliminated from contention.
The Fire had gone three games unbeaten heading into the night, but have picked up just 28 points through 30 games.