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.
Millions of Getty images now available for free via embed tool
Aaron Carter is still in love with Hilary Duff