Magee joined the Fire May 25 and scored 15 goals and assisted on four others in 22 games for Chicago. He earlier scored six goals for the Los Angeles Galaxy, giving him 21 for the season. That was one off the league-leading total of 22 by Camilo Sanvezzo.
Magee is the first Chicago player to win the MLS MVP award.
The award is decided through a vote of MLS club management, players and media.
Robbie Keane, Magee's former Galaxy teammate, came in second while Montreal's Marco Di Vaio was third and New York's Tim Cahill was fourth.