Playing his second game with San Jose since being acquired from Toronto FC as part of a four-player trade last month, Gordon came off the bench in the 56th minute and scored on a header 11 minutes later.
Kenny Cooper scored in the 23rd minute for the Timbers after slipping through the San Jose defense and tallying on a left-footed tap-in at the near post.
The Earthquakes (5-8-10) remained a point behind seventh-place Portland (7-10-5) in the Western Conference standings with the draw.
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