Referee Kevin Stott waved play to continue because the ball was actually sent toward the RSL goal by midfielder Sunny. Nikolic was alone with RSL keeper Nick Rimando and easily slotted home.
Coach Jeff Cassar argued to fourth official Nima Saghafi that Nikolic was offside, not realizing what happened.
"At the time it happened, I didn't know that Sunny had nicked the ball, I thought they had sent it through," Cassar said.
Center backs David Horst and Justin Schmidt were caught flat-footed and Rimando had no chance.
"The lineman put his flag up and the ref put his whistle to his mouth and did the play on thing," Horst said. "When the ref puts his whistle to his mouth, you think he's going to blow it and he didn't. Like they say, you gotta play to the whistle and we didn't."
Only four minutes later, Fire midfielder Arturo Alvarez cut in from the right side and his shot from just outside the box deflected in off Horst. It went past Rimando's left side, as the keeper was wrong-footed headed to his right.
"We knew going into the game that he's all left foot; the scouting report was don't let him cut back, and I think we let him cut back four times on that play," Horst said.
Making matters worse, Jordan Allen exited in the 27th minute with a right quad strain to add to RSL's injury woes. He was replaced by Ricardo Velazquez.
Defenders Chris Shuler (foot) and Justen Glad (knee) were both out, with Cassar opting to give Schmidt his first career start. In addition, Joao Plata was out with a hip injury with Luis Silva making his season debut.
On a 28-degree day that was the coldest home opener in Chicago history, Cassar inserted Luke Mulholland to start the second half for Sunny but his club remained goalless. RSL controlled play for most of the remainder of the game, but Albert Rusnak had a volley in the 51st blocked by Fire defender Michael Harrington, and Yura Movsisyan had a golden opportunity in the 78th minute go wide.
"I thought the offensive push was there, the intent was there, the final execution wasn't there," Cassar said. "Chicago did a really good job of clogging up that middle there and making the box tight."