The Astros blew a 3-0 lead in the seventh when New York's Kirk Nieuwenhuis capped a three-run rally with a two-run single off starter Bud Norris.
Fernando Rodriguez (1-3) earned the victory after getting the final out in the eighth and Brett Myers notched his fifth save for Houston, which claimed the opener of a three-run set at Minute Maid Park.
Matt Downs smacked a two-run homer for the Astros.
New York starter R.A. Dickey allowed three runs on three hits over six innings.
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