Cristian Roldan and Will Bruin scored to lift the Sounders to the summit in the west, leapfrogging hosts Sporting KC.
Sporting KC was on a three-game winning streak against Seattle – the longest active winning run against the Sounders as no team had won four in a row versus the franchise since San Jose Earthquakes in 2012-2013.
But Seattle ended that skid against Sporting KC – Roldan opened the scoring in the 31st minute at Children's Mercy Park, where the Sounders star got on the end of Brad Smith's cross.
Bruin doubled the lead against the run of play 10 minutes into the second half after heading home at the far post.
Entering the fixture, the Sounders conceded an MLS-low 20 goals this season, with opponents scoring with just 7.2 per cent of their shots, also lowest in the league. Seattle had also outperformed their expected goals against by 8.1 this season (20 conceded, 28.1 expected).
The Sounders were breached by Johnny Russell on the hour mark, but Seattle held on for victory to sit two points clear of Sporting KC in the west.
Elsewhere, Austin – bottom of the Western Conference – stunned fifth-placed LA Galaxy 2-0, while Chicago Fire held second-placed Nashville to a 0-0 draw in the east.