Down 4-3, Atlanta struck in the eighth against Schoeneweis (2-5) and three Mets relievers. It was the latest collapse for a beleaguered bullpen missing injured closer Billy Wagner.
Carlos Delgado hit a two-run homer in the Mets ninth off Mike Gonzalez. But the right-hander with the unusual rocking motion struck out the next two batters for his 13th save in 15 chances.
The Mets lost two of three in the series against their longtime nemesis, and now head back to Shea Stadium for their final seven games.
Atlanta once again got in the Mets' way to reach the postseason.
The Braves were 8-1 against New York this year at Turner Field; Philadelphia went 9-0 at the ballpark.
Schoeneweis retired the first batter in the eighth, then Omar Infante doubled. Casey Kotchman tied it with a checked-swing, bloop single.
Joe Smith relieved and Jeff Francoeur hit an RBI triple for a 5-4 lead. Pedro Feliciano pitched next, and got one out before issuing an intentional walk. That brought on Aaron Heilman and, after another intentional walk, Martin Prado delivered a two-run double.
Jorge Julio (3-0) got the win with a scoreless eighth.
The Mets, 4-6 in their last six games, had won the opener of the three-game series 9-5 on Friday night before losing 4-2 Saturday night.
After an embarrassing collapse last year in which they failed to hold a seven-game lead with 17 remaining, the Mets held onto first place just one day before giving it back to Philadelphia this weekend.
The Mets took a 4-1 lead in the second on David Wright's 32nd home run. Wright connected after pitcher Mike Pelfrey drew a walk from James Parr.
New York scored a pair of runs in the first on an RBI double by Delgado and a bases-loaded walk to Luis Castillo.
Infante was hit with a pitch with the bases loaded in the first inning for the first Brave' run, but Pelfrey got out of the jam by getting Kotchman to hit into an inning-ending double play.
Atlanta added a run in the second on an RBI single by pinch-hitter Ruben Gotay and got within 4-3 in the seventh on a sacrifice fly by Prado.
