Houston got the decisive tally in the 57th. Hainault's header from the right side of the six-yard box found the net after a corner kick and Houston held on to win a rematch of the 2011 MLS Cup.
The Dynamo ran their unbeaten streak to four games.
The defending MLS champion Galaxy (3-8-2), meanwhile, stretched their own winless skid to seven straight contests.
Edson Buddle scored for Los Angeles.
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