Eddie Johnson scored in the opening minute and had an assist on Alonso's goal to help Seattle (9-5-7) extend its unbeaten streak to 2-0-3.
Drew Moor scored his third goal of the season in the 3rd minute for Colorado (7-14-1). The Rapids have been outscored 11-3 during their skid.
On the tiebreaking goal, Alonso broke free of midfielder Wells Thompson, took Johnson's cross and buried a shot past Colorado goalkeeper Matt Pickens.
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