Instead, they are in second place in the National League East for the first time in more than a year.
The 5-1 Braves, who were dethroned by the Mets last season after 14 consecutive division titles, are alone on top for the first time since last April 5.
"We'll take a 4-2 trip, but it could have been better," Mets manager Willie Randolph said after Sunday's 3-2 loss at Turner Field.
Sloppy defense betrayed the Mets in Saturday's 5-3 loss. In the series finale, it was the bullpen. In both games, Randolph's team was unable to get clutch hits.
"We gave away a couple of games," the manager said. "When you play a good ballclub and don't execute the little things, that is what happens."
Thanks to consecutive homers by Shawn Green and Ramon Castro in the second inning off Kyle Davies, the Mets led, 2-1, going into the bottom of the eighth. But Aaron Heilman couldn't hold the advantage.
The Mets' bullpen hadn't given up a run this season, and Heilman hadn't allowed a baserunner in two appearances covering an inning.
"The bullpen had been superb," Randolph said.
Not this time, though.
Chipper Jones, who was 4-for-10 with two homers against Heilman coming in, led off the decisive rally with a double on a 3-2 pitch.
Heilman then struck out Andruw Jones, but then Brian McCann and Jeff Francoeur had consecutive RBI doubles to put the Braves on top.
"It's a tough loss," Heilman said. "We had the lead, and you feel like we should win these games."
"He missed his location, obviously," Randolph said of Heilman's eighth-inning problems.
"It was up -- certainly not a quality pitch," Heilman said of the opening fastball that McCann hit to the opposite field to tie the game. "It was a mistake."
McCann is known for using the whole field. The free-swinging Francoeur isn't. But he went the other way with a 2-2 offspeed pitch for the game-winning RBI double.
"[Heilman] always comes hard with that little sinker, so I just wanted to get something I could go to right field with," Francoeur said.
"Unfortunately, it was one of those days where I felt better than the results that I got," said Heilman, who ended the seventh inning by getting Edgar Renteria to tap out with runners at second and third.
Randolph didn't put the loss on his pitchers, but rather his hitters. The Mets, who won the series opener on Friday against the Braves, 11-1, were 0-for-8 with runners in scoring position a day after leaving 13 runners on base.
Jose Reyes, who had his third triple in two days in the fifth inning, opened the game with a walk off Davies, stole second and moved to third on a balk. But he was stranded there as Jose Valentin grounded out and Carlos Beltran and Carlos Delgado struck out.
Orlando Hernandez allowed just one other hit after a first-pitch homer to Kelly Johnson leading off the bottom of the first inning, but left for a pinch-hitter in the seventh after six strong innings.
"I felt good," said Hernandez, who didn't question Randolph's decision, despite his having thrown just 91 pitches. "It was the right move."
With a runner on second and two outs, Julio Franco drew a walk. But Chad Paronto replaced Davies and got Reyes to pop out.
The Mets left two more runners on in the eighth inning, then went down 1-2-3 against Braves closer Bob Wickman in the ninth. Wickman has three saves and a win.
On Monday, the Mets open their next-to-last season at Shea Stadium. John Maine will pitch against Phillies left-hander Cole Hamels in the 1:10 p.m. ET game.
"I'm looking forward to getting home," Randolph said.
Guy Curtright is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.