Beltran, hitting .400, was 2 for 3 with a walk in New York's first visit to Atlanta this year. The two homers gave him four this season.
John Maine (2-2) earned his second consecutive win despite setting a career high with six walks. Francisco Rodriguez pitched a perfect ninth for his sixth save.
Javier Vazquez (2-3) gave up a season-high six runs in 6 2-3 innings. Chipper Jones homered for Atlanta.
Vazquez allowed seven hits, including the three homers - each to center field. The Braves led the major leagues with only 11 homers allowed before facing the Mets.
New York left-hander Oliver Perez was tied for the National League lead with 21 walks when he was sent to the bullpen on Monday. Maine is not far off the lead with 18 walks, including four in the first two innings.
Maine gave up three hits and three runs in six innings. He had a season-high seven strikeouts.
The Braves took a 3-0 lead in the second against Maine, who issued three walks in the inning.
With one out and the bases loaded, shortstop Jose Reyes fielded Vazquez's grounder and flipped to Luis Castillo for one out as Jeff Francoeur scored from third. Castillo's throw to first was wild, allowing Brandon Jones to score on the error.
Yunel Escobar added a run-scoring single after Maine's third walk of the inning.
The Mets took the lead on four hits, including two-run homers by Beltran and Wright, in the sixth. Beltran's shot drove in Daniel Murphy, who led off the inning with a single. Wright's homer drove in Carlos Delgado, who had a single to left in his return from a sore right hip.
Delgado was 1 for 4 in his first start since April 26.
Beltran's second two-run homer knocked Vazquez out of the game with two outs in the seventh.
Jones hit an 0-2 pitch from J.J. Putz into the Braves' bullpen for his third homer in the eighth, cutting New York's lead to 6-4.
He has a .329 career batting average against the Mets, including 40 homers.
Notes: Mets manager Jerry Manuel said Perez will move to the bullpen and 40-year-old rookie LHP Ken Takahashi will start Friday against Pittsburgh. Manuel said there is no timetable for Perez returning to the rotation. ... Maine had five walks in a game four times, most recently on April 22 in a 5-2 loss at St. Louis. ... Beltran had his first multihomer game of the season and the 26th of his career. ... Braves LHP Tom Glavine reported no problems after throwing in the bullpen for the first time since inflammation was found in his left rotator cuff three weeks ago.
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