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.
McPhee, Cokas 'working on their marriage' after affair
LGBT community has 'bullied the American people': Bachmann