Henry Blanco and Kevin Millwood also added RBI singles in the third.
Mark DeRosa, a childhood fan of the Mets growing up in New Jersey, added a solo home run to lead off the fourth.
After trailing 6-3 on Tuesday night, Atlanta had scored then fifteen unanswered runs.
Kevin Millwood (17-6) continued his resurgence, stifling batters all day long and won his eighth straight decision. He was able to go 5 2/3 innings, allowing six hits, one run, three walks, and seven strikeouts.
Trachsel (9-11) got the loss after pitching 2 1/3 innings while giving up four runs before leaving the game after being hit on his pitching hand by an Andruw Jones ground ball up the middle. He was diagnosed with a contusion of the right thumb and x-rays were negative.
John Valentin got the Mets on the board with a pinch hit single in the top of the sixth that knocked out Millwood. That was Valentin's thirteenth RBI as a pinch hitter this season.
Edgardo Alfonzo added his 15th home run, a solo job in the eighth off Tim Spooneybarger.
Chipper hit his second home run of the game in the eighth. It was a two run shot to right field off reliever Satoru Komiyama.
In the ninth, the Mets scored three runs, including a Mike Piazza double to score two runs but the rally fell short after John Smoltz came on and nailed it down for his 50th save of the season.
Notes- Brady Clark, part of the Shawn Estes deal, joined the team today.
-Grant Roberts who came off the DL last night did not pitch.