The two-time defending MLS Cup champions also won for the third time in three games at Toyota Park, and handed the Fire (5-2-1) their second loss at home this season.
Ricardo Clark scored for Houston in the 17th minute when the ball deflected off the foot of Fire midfielders Chris Rolfe.
Calen Carr tied it when he beat Dynamo goalkeeper Pat Onstad on a header in the 28th that gave Cuahtemoc Blanco his second assist.
The Fire gave up more than one goal for the first time this season.
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