Seattle were dominant in the first half but were frustrated by Colorado on a number of occasions.
Fredy Montero and Scott were both guilty of wasting clear chances to put Seattle clear in the first period.
Colorado's Matt Pickens produced a string of impressive saves to keep his side in the match but Seattle were not to be denied for much longer.
An Alex Caskey corner was headed in by Scott following a lack of marking inside the six-yard box.
The Rapids were forced to change their game plan but failed to unlock the Sounders defence and the home side held on to secure the points.