Striker Fanendo Adi scored his first two
Portland improved to 3-3-7, winning its second straight game and third in its last five.
Chivas USA dropped to 2-6-4.
Former Chivas midfielder Jorge Villafana helped create the first goal when he ran down the left flank in the 65th minute and crossed the ball to Adi for a shot from 10 yards.
Adi scored in the 71st minute on a breakaway.
Chivas USA's Bobby Burling was ejected in the 84th minute after a rough challenge on Adi.
The Timbers held a 65% to 35% advantage in possessions in the first half and had five shots on goal to one for Chivas USA, forcing Dan Kennedy to make three saves.