The Braves, having already clinched one of the National League's wild card berths, had a five-game winning streak snapped.
Niese (13-9) went seven innings and allowed Atlanta's only run -- a homer by Freddie Freeman in the fourth.
The New York bull pen did not allow a hit over the final two innings with Bobby Parnell retiring the side in the ninth on just six pitches for his sixth save.
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