Medlen (12-12) allowed one run on seven hits and didn't issue a walk in the 95-pitch effort, winning for the third time in three starts.
Andrelton Simmons smacked a two-run homer and Evan Gattis added a solo shot to provide the Braves' scoring.
Mets starter Carlos Torres (3-3) yielded three runs on seven hits over seven full innings.
Daniel Murphy drove in New York's only run.
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