Miller gave Vancouver the advantage in the 4th minute, receiving a long pass from Corey Hertzog, cutting back to his right and sending a right-footed shot into the bottom right corner of the net.
The Whitecaps' Darren Mattocks made it 2-0 in the 79th minute when he settled a headed pass from Gershon Koffie and lifted a volley over the head of Sounders goalkeeper Michael Gspurning.
Vancouver (8-5-5) extended its unbeaten streak to five games in the Cascadia Cup contest, marking its initial win over the Sounders since joining the MLS in 2011.
Seattle fell to 7-6-3.
Swim Week Miami Beach 2014 [PHOTOS]