That brought up Nieuwenhuis, who belted a pitch off the facing of the upper deck in right field for a game-winning, three-run shot as the Mets salvaged one victory in their three-game home series.
The rally made a winner of Bobby Parnell (5-3), who had tossed a scoreless top of the ninth.
Chicago starter Matt Garza hurled seven shutout innings in a no-decision, holding the Mets to three hits while walking two and striking out five.
Alfonso Soriano drove in a run for the Cubs.
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