McCann's two-run double highlighted a four-run third inning that broke the game open and his blast in the fifth staked the Braves to a 7-1 lead.
Kris Medlen (8-1) won his sixth straight outing, yielding two runs on four hits in six innings as the Braves clinched their three-game series.
Mets starter Jeremy Hefner (2-6) was roughed up for five runs on eight hits over just 2 2/3 frames.
Lucas Duda knocked in a pair of runs for New York.
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