Fernandez (10-5) extended his unbeaten streak to eight starts, scattering four hits in seven scoreless innings while lowering his ERA to 2.30, third-best in the National League.
The rookie right-hander didn't issue a walk and struck out eight in the 97-pitch performance.
A.J. Ramos hurled a scoreless eighth and Steve Cishek logged his 28th save for Miami, which rebounded from a 3-2 loss in Friday's three-game series opener.
The Marlins scored all three of their runs in the fourth inning on RBI from Ed Lucas, Adeiny Hechavarria and Jake Marisnick.
Colorado's Jeff Manship (0-4) was hung with the loss, surrendering three runs on four hits over six innings.
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