Chicago's Gonzalo Segares ran back toward the goal to clear the ball and instead knocked it into the net.
Lamar Neagle also scored for Seattle (14-8-4), which has won seven of its last eight.
Mike Magee had a goal for the Fire (10-11-5), which has never beaten the Sounders while losing for the fourth straight time in Seattle.
Magee gave the Fire a 1-0 lead in the 25th minute on a left-footed kick from the center of the box off an assist from Dilly Duka. Magee, who didn't play in the second half, broke free behind the defense to receive the ball and shot it past goalkeeper Michael Gspurning for his 15th goal.
Seattle's Osvaldo Alonso missed a penalty kick in the 30th minute that goalkeeper Sean Johnson punched away. A hand ball in the penalty area by Bakary Soumare off a corner kick set up the attempt.
Neagle blasted a left-footed kick in the 40th minute off an assist from Marc Burch to tie the score.
Johnson had saves early in the second half on Seattle shots by Alonso and Obafemi Martins, who returned after missing four games with a sprained ankle. Johnson made a diving save on a shot by Alonso in the 50th minute.
Martins shot wide on a header in the 83rd minute.
Seattle's Clint Dempsey and Eddie Johnson missed the game while training with the U.S. national team for Tuesday's game against Mexico in Columbus, Ohio.