Ryan Johnson opened the scoring after 15 minutes for the Timbers and Darlington Nagbe added a second for the visitors with 23 minutes to play.
But the Sounders grabbed a lifeline with a 90th-minute goal from Osvaldo Alonso, giving the side a bit of hope ahead of Thursday's second leg in Portland.
Jack Jewsbury set up the first goal when he got down the right wing and drove the ball to the near post for Johnson, who beat goalkeeper Marcus Hahnemann with a glancing header.
Clint Dempsey was easily the most dangerous man for Seattle, but he endured a night of near misses, with his first good chance clipping the top of the crossbar from a 25-yard free kick.
Kalif Alhassan came off the bench in the second half for the Timbers and he needed just six minutes to make his impact as he fed a ball into the area for Nagbe, who turned past a defender with a nice touch and fired his shot beyond the reach of Hahnemann.
Dempsey then sent a volley whistling inches past the post before he saw a header hit the crossbar in the 87th minute.
It looked like it wasn't going to be Seattle's night, but Alonso popped up with a well-struck volley from 12 yards to give the Sounders some life ahead of Thursday's return leg.
11/03 00:21:38 ET