Fernandez (3-3) scattered three hits and struck out eight in breaking a personal three-start winless streak.
The 2011 first-round Marlins draft pick issued just one walk and supplied a run-scoring single in the second for a 2-0 Miami lead.
Chris Coghlan added three hits, including two run-scoring singles, while Derek Dietrich and Adeiny Hechavarria each drove in two runs as the Marlins clinched their three-game series.
Mets starter Collin McHugh (0-1) was charged with the loss in a spot start for the injured Jonathon Niese, surrendering four runs on six hits over four frames.
Justin Turner got the only RBI for New York.