Figueroa (3-8) threw 113 pitches without a walk and struck out seven in his first career shutout.
Josh Thole led New York with three hits and one RBI, a run scored on a fourth-inning fielder's choice and Angel Pagan had four of the nine hits for the Mets, who finished 22 games under .500 (70-92).
The Astros finished the season with five losses in their last six games.
The losing pitcher was starter Wilton Lopez (0-2).
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