Chris Johnson hit a three-run homer in the fourth to put the Braves in front, but the Mets tied the game in the top of the fifth thanks in large part to a throwing error by Atlanta starter Kris Medlen.
Atlanta came right back in the bottom of the inning to regain the lead for good.
Freeman went to second on the miscue and scored on a double from B.J. Upton.
Despite committing the error that allowed two unearned runs to score in the fifth, Medlen (4-7) picked up the win. He struck out seven and gave up six hits in seven innings. Craig Kimbrel struck out two in a perfect ninth for his 20th save.
The Mets had won the opening two games of this four-game series.
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