The visitors came off the blocks the quicker of the two teams and went ahead after just eight minutes.
Released by Shalrie Joseph, Nick LaBrocca found the target from the centre of the penalty area with his left foot.
The Chivas goal spurred Sounders into action, as they created a number of chances but failed to capitalise on them.
The home side eventually equalised in the 29th minute when Eddie Johnson headed home Christian Tiffert's delivery
Sounders continued to craft chances but left it late to score the winner.
Johnson was again at the right place at the right time when he headed home Fredy Montero's cross from close range in the 89th minute.