Santos' fifth goal of the season came in the 10th minute at rainy RFK Stadium on a header off an assist from Chris Pontius.
He later broke a 2-2 tie with another header in the 70th minute, this time off a Daniel Woolard assist.
Woolard also set up a goal by 2011 league MVP Dwayne De Rosario for United (4-2-3), which snapped a five-game winless streak against Houston.
Will Bruin scored twice for the Dynamo (2-2-2).
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