Fernandez (10-5) allowed four hits and did not walk a batter as he lowered his ERA to 2.30. Fernandez has been one of the best pitchers in the Majors since June 1, compiling a 1.52 ERA and 112 strikeouts in 15 starts.
A.J. Ramos pitched the eighth and Steve Cishek earned his 28th save in 30 chances.
Todd Helton had two hits for the Rockies to move into 96th place on the career hit list with 2,496 in 17 seasons, all with Colorado.
The Marlins scored three runs in the fourth off Jeff Manship (0-4).