Martins atoned for his error in the 31st minute when he collected Brad Evans's cross at the near post and managed to fire an effort through Johnson and into the net.
The Sounders were handed the chance to double their lead when Jhon Kennedy Hurtado was sent off for a second bookable offence for bringing down Martins in the area. The striker took the spot kick and slotted the ball into the bottom corner.
Seattle were then reduced to 10 men when Martins was shown a red card for apparently striking Benji Joya in the aftermath of the Fire's goal.
Quincy Amarikwa had the chance to bring his side level in the 59th minute as Joya's shot deflected into his path six yards from goal, but Frei made a fantastic point-blank stop to keep his side ahead.
The Sounders responded to this threat as they found the net for the third time when Lamar Neagle took control of a loose ball in the box and placed an effort into the top corner with a stunning strike.
Chicago weren't done as they rallied back through Shipp, who blasted an effort into top corner from the edge of the box.
Juan Luis Anangono had the chance to earn a point for the Fire late on, but his low shot was well saved by Frei as the Sounders secured the win.