Nagbe broke a 1-1 deadlock in the 33rd minute, firing a hard shot high into the net after receiving an accurate feed from Valeri.
The Portland midfielder also set up a 26th-minute score by Ryan Johnson as the Timbers (9-3-11) kept pace in the Western Conference playoff race.
Mauro Diaz scored for FCD (8-7-9), which extended its winless streak to 11 games.
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