Frederic Piquionne (12) and Will Johnson (45) scored in the first half, before substitute Ryan Johnson (84) added a third late on.
With 30 points, the Timbers went ahead of Real Salt Lake in the Western Conference and Supporters' Shield standings.
Conor Casey scored twice as the Philadelphia Union beat 10-man New York 3-0 to leapfrog the Red Bulls in the Eastern Conference.
Casey scored in the seventh minute, then again in the 64th after Lloyd Sam had earned a straight red for a studs-up challenge, and Antoine Hoppenot added a third two minutes from the end.
Gyasi Zardes scored the only goal a minute before the break as the Los Angeles Galaxy won 1-0 at Chivas USA in the SuperClasico.