Alvarez (4-4) went seven innings, scattering four hits without a walk and striking out five, while tossing 67-of-100 pitches for strikes.
Chad Qualls turned in a 1-2-3 eighth and Steve Chisek struck out the side in the ninth for his 30th save for the Marlins, who fell to the Mets 4-3 in Friday's opener of a four-game series.
Donovan Solano smacked a solo homer and Logan Morrison drove in a pair of runs for Miami.
Carlos Torres (3-5) yielded two runs on three hits over six innings for the Mets.
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