Wagner escaped a major jam in the ninth inning and Moises Alou hit a tiebreaking homer in the eighth to help New York edge the Braves 4-3 on Wednesday.
Wagner earned his 350th career save and extended his scoreless streak to 21 innings when slumping Andruw Jones grounded into a game-ending double play. Jeff Francoeur bounced into a force play at the plate for the first out of the inning.
"I made two good pitches, one to Francoeur and one to Andruw and that's all I needed tonight," Wagner said. "There's always a way to get out of it and tonight we proved it."
Shawn Green went 4-for-4 for the Mets, who beat Atlanta for only the fourth time in 11 meetings this season. Luis Castillo's broken-bat, two-run single off reliever Ron Mahay tied the score with two outs in the seventh.
By rebounding from a 7-3 loss Tuesday night, the NL East leaders increased their cushion over the Braves to 4 1/2 games. Atlanta, which had won three straight overall, fell to third place, a half-game behind Philadelphia.
"It was a big game, a huge game. We got a great performance from El Duque and a big hit from Castillo," Green said.
A pair of 12-game winners will start the deciding game of the series Thursday afternoon, with Tim Hudson opposing New York's John Maine.
After an early pitchers' duel between John Smoltz and Orlando Hernandez, the Braves went ahead 2-1 in the sixth on a two-out, two-run double by Mets nemesis Chipper Jones. Mark Teixeira followed with an RBI single.
On a 93-degree evening at Shea, Wagner entered in the ninth with a 4-3 lead. But Chipper Jones and Teixeira hit consecutive singles before the closer walked pinch-hitter Chris Woodward, who was squaring around to bunt.
Francoeur, on a recent tear, hit a grounder to third baseman David Wright for an out at the plate. Andruw Jones, struggling through a poor season and dropped to seventh in the lineup for the second time this year, then hit a grounder to Castillo at second for a tailor-made double play.
Andruw Jones also grounded into an inning-ending double play in the fifth and finished 0-for-4, dropping his batting average to .215.
"He's a good hitter. He should break out. We're waiting," Braves manager Bobby Cox said.
The victory preserved, Castillo did a jubilant little dance with shortstop Jose Reyes. It was Wagner's 26th save in 27 chances this season. He has not permitted a run in 19 outings since June 15.
"Set the table, just didn't clear it," Chipper Jones said. "Nobody to kick but ourselves."
After two long flyouts earlier in the game, Alou drove an 0-2 pitch from Rafael Soriano (2-3) over the left-field fence.
"My previous couple at-bats, I felt more comfortable at the plate. I trusted my hands," Alou said.
Aaron Heilman (7-3) worked a scoreless eighth for the win, becoming the first Mets pitcher to beat Atlanta this season other than Oliver Perez.
Wright hit a sacrifice fly in the first off Smoltz, who left with a 3-1 lead. He was charged with three runs _ two earned _ and eight hits in 6 1-3 innings.
"That's the toughest one of the year so far," Smoltz said. "They found every hole."
Cox said Smoltz tweaked his back in the sixth, but it was nothing serious.
Hernandez allowed three runs and four hits in seven innings. He didn't give up a hit until Brian McCann's leadoff single in the fifth.
Notes: Mets RHP Pedro Martinez gave up five runs and six hits in three innings for Class-A St. Lucie against Lakeland, his first minor league rehab start as he attempts to return to New York's rotation after offseason shoulder surgery. The three-time Cy Young Award winner struck out five and threw 44 of 63 pitches for strikes. He did not walk a batter, but allowed two homers. ... The gametime temperature was the highest at Shea Stadium since a 98-degree day on Aug. 9, 2001, against Milwaukee. ... The Mets have won El Duque's last six starts and eight of his past nine. ... New York improved to 15-6 in one-run games. ... Green is 16-for-29 (.552) against Smoltz.