Sebastian Blanco set up both goals for the Timbers against the Rapids, first helping Jeremy Ebobisse get the club on the board and then setting up Diego Valeri to double the lead.
The Rapids had a penalty overturned in the second half, helping dent the club's cause as a the club struggles to close out a rough season.
Felipe Gutierrez scored the game's only goal, his first league goal since March, to give his side a timely win.
SKC returns to action next week against the bottom team in the West, the San Jose Earthquakes, but also faces a closing run that includes direct rivals for one of the top two places in the conference in FC Dallas and LAFC.
In the Eastern Conference David Villa scored a late free kick to earn a 1-1 draw for New York City FC against D.C. United.
The result secured a playoff spot for Atlanta United due to D.C. dropping points.