Playing in his 17th career MLS game, Stojanovic notched his first career two-goal game with a pair of impressive plays and scored for the first time since May 22.
The biggest game of Stojanovic's brief MLS career helped Chicago get its first win since July 7 and avenged a 2-0 loss at Red Bull Arena on May 1.
The 27-year-old midfielder made it 1-0 in the second minute by finishing off a nice passing sequence. After getting a pass from Chinonso Offor, Stojanovic scored on a right-footed shot from the center of the box that whizzed by multiple defenders and past New York goalkeeper Carlos Coronel, who attempted to make a diving save before the ball ended up in the right side of the net.
Six minutes later, Chicago scored off a throw-in from defender Carlos Teran. A New York defender headed the ball to Stojanovic and he finished it off by putting another right-footed shot by Coronel, and that was enough.
Chicago goalkeeper Bobby Shuttleworth made three saves despite New York maintaining possession for 62.3 percent of the match. Shuttleworth nearly notched his 48th career clean sheet and third this season until Tom Barlow scored in the final minute of stoppage time off a rebound on a free kick.
Coronel made one save.
New York saw its winless skid reach six games (0-3-3) since beating Orlando City on July 3.
After Stojanovic's dynamic goals, Chicago nearly took a 3-0 lead but Fabian Herbers had an open look sail off the post in the 60th minute. New York nearly made it a one-goal game a few minutes later, but Patryk Klimala had a shot in the box deflected by Teran before it reached the net.
Shortly after helping Chicago maintain the shutout, Teran was taken off the field on a stretcher.
Before getting its goal in the final minute, New York missed two chances to score.