The Marlins lost their fourth straight game and their next setback will be their 80th of the season.
Ryan Wheeler came up with two away in the inning and he brought home Cuddyer with a double.
That quick rally gave the win to starter Jhoulys Chacin (12-7), who gave up a sacrifice fly to Greg Dobbs in the seventh that briefly put the Marlins in front.
Rex Brothers struck out two in a perfect ninth for his 12th save.
Colorado had lost its previous two games, having blown ninth-inning leads to Philadelphia in both of them.
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