With the tying run on third and one out in the ninth, Steve Cishek got Chris Young to hit a fly ball to left field that appeared deep enough to tie the game, but Marcell Ozuna's second throw home (and assist) of the night beat Kirk Nieuwenhuis to the plate to end the game.
Miami got on the board against Mets starter Daisuke Matsuzaka in the bottom of the first. Rafael Furcal led off the frame with a triple, and Adeiny Hechavarria followed with an RBI groundout to give the Marlins a 1-0 lead.
Henderson Alvarez, as he was in his two previous outings against the Mets, was solid despite aggravating a hamstring early in the game. Alvarez landed awkwardly following through on a strikeout and was pulled after six and a third innings.
Alvarez yielded seven hits and recorded seven strikeouts while not giving up a run.
Despite failing to capitalizing on a first and third opportunity in the sixth, the Marlins added a pair of runs against Mets reliever Vic Black in the seventh. Jake Marisnick singled and stole second and third base, and Marisnick came around to score after Anthony Recker's throw sailed into left field.
A Hechavarria groundball that took a hop over David Wright's glove at third base allowed Justin Bour to score, giving Miami a three run edge.
Kevin Gregg struggled out of Miami's bullpen in the eighth, and after Wright and Eric Campell added RBI singles, Mike Dunn was able to get out of the jam after Marcell Ozuna's throw home caught Wright trying to tie the game.
Miami will look to take the series lead in game three of the four game set on Saturday.
Hero of The Game: Henderson Alvarez (+.332 WPA)
Goat of The Game: Kevin Gregg (-.162 WPA)
Play of The Game: David Wright singled to center. Chris Young scored. Eric Young advanced to third base. (.115 WPA)