The Whitecaps took the lead in the fourth minute when Kenny Miller latched onto a long ball and beat his man before firing a low shot into the bottom corner.
Corey Hertzog nearly added a second for the home side when he turned and shot with his right foot on the edge of the area, but Michael Gspurning palmed his effort past the post.
Seattle could have been level but Brad Knighton made two brilliant reaction stops to deny Zach Scott's efforts at goal from inside the six-yard box.
After the break the Sounders were denied again, this time by the woodwork as Lamar Neagle's shot was deflected onto the post by Brad Rusin.
A second goal finally came for Whitecaps on 79 minutes through substitute Darren Mattocks, who finished well to confirm the victory for the home side and move them up to fourth in the table.