Marcelino Moreno put the Red and Black in front in the 17th minute and it looked to be enough until a second-half stoppage time goal by Gudmundur Thorarinsson rescued the Boys In Blue.
Story of the match
The Boys In Blue started brightly, Keaton Parks forcing Brad Guzan to tip the ball over for a corner from a powerful strike in the seventh minute.
The hosts took the lead two minutes later when a turnover on the halfway line allowed Atlanta to counter through Luiz Araujo, the Brazilian playing it to Moreno, who beat Sean Johnson.
Johnson was called into action as he stopped a 37th-minute free kick by Araujo.
NYCFC had a chance to restore parity right on half-time, but Medina’s free kick was cleared away from danger.
Cubo Torres got an early look at goal that was well parried by Johnson. That was followed up in the 55th minute by a chance for George Bello that crashed against the crossbar.
At the other end, a free kick from Medina landed on the head of Alexandre Callens, but he was unable to keep his effort down.
Santiago Rodriguez was introduced in the 62nd minute and just three minutes later, he fired off a strike from distance to test Guzan.
In the 89th minute, Talles Magno won a free kick from a dangerous position. Thórarinsson took it and he curled in a sensational effort past Guzan to tie the game.
Man of the match: Gudmundur Thorarinsson
He only played half an hour, but he may have scored the most critical goal of the season, ending NYCFC's 509-minute goalless drought and earning the Boys In Blue a point that could go a long way towards carrying them to the playoffs.