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.
Beautician charged with giving client fatal silicone butt injection
McPhee, Cokas 'working on their marriage' after affair