After six minutes of added time, the Fire thought they'd leveled it when Wyatt Omsberg headed it in before the goal was overturned due to offside after a video review.
Luka Stojanovic scored on a free kick in the 69th minute.
Edison Flores scored his first MLS goal in the seventh minute and D.C. United beat the Chicago Fire 1-0 on Thursday night.
Corey Burke and Jakob Glesnes scored goals nine minutes apart.
It was coach Gerhard Struber's first win and goalkeeper Carlos Coronel's first shutout with New York.
Chicago tied the game in the opening minute of the second half on Luka Stojanovic's second goal of the young season, taking advantage of a sloppy effort by Atlanta's back line.
Soccer fans will soon be able to see the Chicago Fire play in person.
The Montreal Impact have acquired midfielder Djordje Mihailovic from the Chicago Fire.
Chicago Fire was eliminated from playoff contention after losing to New York City FC 4-3.
Jose Aja and Robin Lod scored in the second half and Minnesota United overcame a two-goal deficit to tie the Chicago Fire 2-2 on Wednesday night.
Cory Burke scored on a header in the 65th minute, helping the Philadelphia Union beat the Chicago Fire 2-1 on Wednesday night.
The New York Red Bulls salvaged a 2-2 tie against the Chicago Fire with a Brian White goal in overtime.
C.J. Sapong scored in his first start in nearly three months, Boris Sekulic had his first MLS goal and the Chicago Fire beat D.C. United 2-1 on Sunday night.
Winston Reid scored his first MLS goal in the 67th minute and Sporting Kansas City beat the Chicago Fire 1-0 on Wednesday night.
Robert Beric scored his fourth goal in four games and the Chicago Fire beat the Atlanta United 2-0.
Gyasi Zardes scored in the 88th minute to help the Eastern Conference-leading Columbus Crew tie the Chicago Fire 2-2 on Saturday.
Teal Bunbury scored twice in the New England Revolution’s 2-1 victory over the Chicago Fire on Sunday night.
Álvaro Medrán and Ignacio Aliseda each scored his first MLS goal, and Chicago beat Cincinnati 3-0 on Tuesday night in the Fire’s first game at Soldier Field in nearly 15 years.
Darlington Nagbe and Gyasi Zardes scored seven minutes apart in the second half and the Columbus Crew beat the Chicago Fire 3-0 on Thursday night.
The San Jose Earthquakes beat the Chicago Fire 2-0 on Sunday to clinch a spot in the MLS is Back tournament round of 16.