After Dominic Oduro had brought the Fire back on level terms following Michael Farfan's opener for the Union, Guatemalan Ruiz struck from 35 yards out, collecting a clearance from his own free-kick and volleying over Chicago keeper Jon Conway.
The victory moves Philadelphia a point clear of the New York Red Bulls who, without injured French striker Thierry Henry, were held to a 2-2 draw at the Houston Dynamo.
The Red Bulls needed an injury-time header from Moroccan-born Mehdi Ballouchy to get a point from their trip to Texas after goals from Brad Davis and Spaniard Sergio Koke had put Dynamo in front.
The L.A. Galaxy won their local derby against Chivas U.S.A 1-0 to stay on top of the Western Conference - Chad Barrett heading in a David Beckham free-kick in the 26th minute for the Galaxy.
The assist was Beckham's sixth of the season but he is now set to miss the Galaxy's midweek match-up with Houston as he will be playing in former Manchester United team-mate Gary Neville's testimonial game in England.
The Seattle Sounders stay second in the West after defender Jeff Parke scored his first MLS goal in seven years, heading home a Tyson Wahl corner kick in injury time, for a 1-0 win over Sporting Kansas City.
Dallas and Real Salt Lake's game on Sunday was delayed, in the 83rd minute, for one hour 40 minutes due to a rain storm but finished 0-0.
