Giancarlo Stanton homered in the sixth, cutting Miami's deficit to 2-1, and Jose Reyes tied it with a sacrifice fly in the next frame.
The rally made a winner of Heath Bell (4-5) while Steve Cishek pitched a 1-2-3 ninth for his 15th save as the Marlins took the opener of a season-ending three-game set.
David Wright and Mike Baxter drove in runs for the Mets.
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