The Mets loaded the bases with none out against Zach Phillips (0-1) and seemed on the verge of wasting the opportunity after Zach Lutz and Andrew Brown each produced a force-out at home plate.
D'Arnaud came through with a single off of Ryan Webb, giving New York its third win in the four-game series against Miami.
Vic Black (1-0) earned the decision after Mets starter Dillion Gee had tossed 7 1/3 shutout innings, allowing six hits and two walks with eight strikeouts.
Marlins starter Tom Koehler yielded three hits without a walk while fanning five in eight innings.
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