Pineda's 84th-minute strike secured a 2-1 victory for Chicago, sending coach Raphael Wicky's side to the top of Group B in the World Cup-style tournament at Orlando, Florida.
But the defeat leaves Seattle, the reigning MLS Cup champions, in a dogfight to reach the knockout stages. Seattle have just one point from two games and are third in Group B, outside of the automatic qualification places.
"It's not good," Sounders coach Brian Schmetzer said when asked about his team's predicament.
"We'll have to make sure we get a result in the last game and then see where we end up."
Schmetzer was frustrated by his team's inability to create more than seven chances throughout the game.
"It's frustrating when you can't generate chances but that's always the hardest thing to get when you're in pre-season," he said.
After a goalless first half, Chicago took the lead on 52 minutes after a defensive blunder by Seattle's Xavier Arreaga allowed the Fire's Slovenian striker Robert Beric in on goal.
Ecuador international Arreaga misjudged the flight of a long ball forward and Beric pounced on the chance to race clear.
The Slovenian then cleverly twisted and turned his way past the covering Yeimar Andrade before blasting his finish past Seattle keeper Stefan Frei.
Seattle got back on level terms in the 77th minute however when Jordan Morris got to the byline and squared a pass for Kenyan midfielder Handwalla Bwana, who finished from close range for 1-1.
But just when it looked as if Seattle had done enough to grind out a point, another defensive lapse cost them dear.
An inswinging corner from Gaston Gimenez was somehow allowed to bounce across the face of goal through a crowded six yard box and unmarked rookie Pineda was on hand at the back post to tuck away the finish.
In other games Tuesday, Chris Mueller scored twice in the opening 10 minutes as Orlando defeated New York City FC 3-1.
Jesus Medina pulled a goal back for New York just before half-time but Tesho Akindele made the game safe for Orlando on 81 minutes, bundling in his team's third from close range.