Valeri scored in the 16th and 29th minutes for a 2-0 Timbers lead.
The Timbers extended their unbeaten streak to eight games and will hold top seed in the West when the MLS playoffs begin next weekend.
Chivas USA (6-20-8) became the 15th club in league history to lose 20 games in a season.
Ukrainian protestors topple Lenin statue [VIDEO]
'SNL': 'Anchorman 2' cast, One Direction sing 'Afternoon Delight' [VIDEO]