San Jose was awarded a penalty kick in the 53rd minute of a scoreless tie when Shea Salinas was taken down by Andrew Jean-Baptise at the top of the area, and Bernardez followed by putting a shot past Timbers goalkeeper Donovan Ricketts.
Lenhart added a much-needed insurance tally for the Earthquakes (7-9-6) in the 58th minute when he slid through the box to put home a free kick by Salinas.
Darlington Nagbe later scored for Portland (8-3-10), which retained second place in the Western Conference despite the loss.
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