San Jose was trailing in the 60th minute when Manny Lagos sent a through ball to Dwayne DeRosario on the left side of the penalty area. Defender C.J. Brown challenged the Canadian international with a sliding tackle but ended up tripping him.
Ekelund stepped up and converted his first MLS penalty kick attempt, beating goalkeeper Zach Thornton with a low right-footed shot. It was the former Danish international's third goal of the season.
The Fire grabbed the lead in the 10th minute on an impressive solo run by 21-year-old rookie midfielder Kelly Gray. The play began when Chicago captain Peter Nowak had the ball knocked away near the midfield circle. Gray ran onto it, making a 30-yard sprint through the center of the defense.
Just outside the box, Gray unleashed a powerful right-footed blast that beat 'keeper Joe Cannon inside the left goalpost for his second goal of the season.
The Earthquakes were without central defenders Jeff Agoos (World Cup duty) and Troy Dayak (hip strain) and used forward Devin Barclay at midfield in place of Ian Russell (Achilles tendinitis).