Heavy rain and lightning delayed the start of the contest for almost 2 hours, but Johnson's header off a Mauro Rosales free kick dented the net in the first half.
The Sounders (12-8-4) won despite fielding just 10 men for the majority of the contest.
Columbus (8-13-5) played without captain and designated player Federico Higuain, who was serving the first of a two-game suspension.
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