On Decision Day, the Timbers came from behind to beat the Vancouver Whitecaps 2-1 and climb to the top of the west.
A second Western Conference success appeared unlikely for the Timbers when they fell behind to a Kendall Waston header just before the half-hour mark.
However, Liam Ridgewell levelled for Caleb Porter's Portland just three minutes later, putting away a rebound to make it 1-1.
Darren Mattocks side-footed in what proved to be the winner in the 48th minute as Portland finished top of the conference.
Reigning MLS Cup champion Seattle finished second, although Clint Dempsey saw red in a 3-0 victory over Colorado Rapids.
The final playoff spot in MLS was decided as the Earthquakes clinched sixth in the Western Conference in thrilling fashion.
Minnesota United twice came from behind to draw level against San Jose, but a 93rd-minute goal from Marco Urena sent the Earthquakes into the playoffs courtesy of a 3-2 victory.
Jozy Altidore and Sebastian Giovinco were on the scoresheet for Toronto, with the latter also drinking a beer thrown onto the pitch by fans.