Chris Johnson's three-run shot in the 10th inning, which followed a controversial call, lifted Atlanta to a 4-1 decision over New York in the finale of a two-game series.
The victory could be costly, though, for the Braves. Outfielder Jason Heyward may miss the rest of the regular season due to a fractured right jaw he suffered in the sixth inning after taking a pitch from Jon Niese to the side of his face.
X-rays taken at a local hospital showed Heyward's jaw was fractured in two places. He is expected to miss 4-to-6 weeks.
Andrelton Simmons roped a base hit with two down against Scott Atchison (3-2) in the deciding frame, and then Freddie Freeman beat out an infield hit near the mound facing Scott Rice -- but replays seemed to indicate he was out by the slimmest of margins. Johnson stepped in and deposited Greg Burke's first offering into the left-field seats for a 4-1 contest.
"We tried to come in on Chris. We'd been doing it all game, and that was basically where I wanted to put it," said Burke. "It was up a little bit. It was off the plate."
Both second baseman Daniel Murphy and manager Terry Collins were ejected for arguing the Freeman play by umpire Jerry Layne.
"All Jerry said to me is that he thought he got it right," said Mets manager Terry Collins. "I went out to protect Murph."
Craig Kimbrel tossed a scoreless bottom of the 10th for his 40th save, while Luis Avilan (5-0) remained perfect with an unblemished ninth.
Freeman finished with three hits and knocked in the other run for the Braves, who earned a split in the set and have won five of seven overall.
Josh Satin's fourth-inning homer was all the offense for the Mets, who have dropped six of their last 10.
The Braves finally dented Niese in the fourth when Simmons slugged a base hit to center, but he was erased trying to stretch it into a double.
New York then took the lead in the home half, as Satin's leadoff shot to left made it 1-0.
Heyward was hit in the face with two down in the sixth, then Simmons and Freeman singled -- the last of which plated pinch-runner Jordan Schafer with the tying run.
"He said he was OK. He got back on the mound, and he knew he had a job to do. You can't help but hope the guy's all right," Collins said of Niese.
It was the second freak injury in the span of a month between these teams. Braves pitcher Tim Hudson was lost for the season after suffering a gruesomely broken ankle while attempting to cover first on an Eric Young hit.
"He never lost consciousness. It's not the ballpark, but a matter of some freak stuff happening in the course of a season. It could happen anywhere," offered Braves manager Fredi Gonzalez.
The Mets couldn't end the contest despite having the bases loaded and two outs in the ninth.
"If you can't dig deep and match them, winning the game is going to be awfully tough," Collins added of his club's wasted chances.
Atlanta's Alex Wood worked six innings, allowing six hits and one run, fanning four with two walks, while Niese exited after seven full frames having given up one run on five hits with nine strikeouts and three walks ... New York fell to 24-28 in day games and 10-17 at Citi Field this season ... The last time the Mets swept a two-game set from the Braves was May 4-5, 2009 at Atlanta ... The last time they accomplished the feat in New York was April 24-25, 1990 ... The Braves made a late roster move, claiming infielder Elliot Johnson off waivers from the Kansas City Royals.