Rookie Brown notched his team-leading seventh goal of the season with a powerful header from close range in the 36th minute, and Buddle made it 2-0 in the 79th off a through-ball from substitute Nick LaBrocca.
The Rapids (10-7-9) moved past Vancouver into second place in the Western Conference.
The Whitecaps (10-8-6) meanwhile, fell for the third time in five games.
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