Magee underwent surgery on Monday to repair a right hip problem, and he is set to spend six to eight months on the sidelines - meaning he may even miss the start of the 2015 season.
"It's unfortunate that Mike will be out for an extended period, but he's been struggling this season with the injuries," Fire coach Frank Yallop said.
"After consulting with our medical staff, we decided that this was the best time for Mike to have the procedure."
Magee has scored seven goals in 17 appearances this season, on the back of winning the MLS' MVP award in 2013 after scoring 21 goals for the season with the New York Red Bulls and Fire.
The 30-year-old had been out of action since Chicago's 1-0 loss to the Montreal Impact on August 16.
Chicago are seven points outside the top-five in the Eastern Conference standings, albeit with a game in hand and eight fixtures to play.
Also on Tuesday, the club brought in French striker Florent Sinama-Pongolle from FC Rostov.
The former Liverpool and Atletico Madrid man, 29, will take an international roster spot.
"Florent is a quality player with experience playing in some of the top leagues in Europe," Yallop said.
"Since he's been training with us for the past few weeks, we've been able to see first-hand the attributes he has.
"I'm pleased that we were able to add him to the squad as we enter the final stretch of the regular season."