The Braves' Derek Lowe took a no-hitter into the seventh before he tired. Lowe gave up two hits and no runs in 6 2-3 innings.
The Marlins went 1 for 8 with runners in scoring position and are 8 for 54 (.148) in those situations during the first six games of their dismal homestand.
Six of the Marlins' seven losses during their slump have been by a single run.
The Marlins trailed 2-0 in the ninth and had been shut out for 24 1-3 consecutive innings when they tied the game one strike from defeat. Mike Stanton hit a two-run single on a 1-2 pitch from Braves closer Craig Kimbrel (2-2) to make the score 2-all.
Stanton continued to second on an errant throw by right fielder Joe Mather, but Ozzie Martinez struck out to send the game into extra innings.
Chipper Jones walked with one out in the 10th against Mike Dunn (4-4), then took second on a single by Brian McCann. Freeman, who had been 0 for 7 in the series, followed with single up the middle.
The Marlins had two on with one out in the bottom of the 10th, but George Sherrill struck out Greg Dobbs, and Scott Linebrink earned his second save in three chances by striking out Gaby Sanchez on a 2-2 pitch.
Sanchez took strike three looking, and replays showed the breaking ball appeared outside. He threw his bat in protest but complained only briefly to plate umpire Andy Fletcher.
Jordan Schafer had two hits and scored twice for Atlanta off Ricky Nolasco, who allowed two runs in 7 1-3 innings.
Kimbrel struck out the first two batters in the ninth, but Logan Morrison walked and took third on a double by John Buck — only the Marlins' third hit. Stanton followed with his hit, the Marlins' first in 12 at-bats with runners in scoring position in the series.
Kimbrel blew a save for the fifth time in 23 chances.
Lowe gave up a walk to start the second, then retired 16 straight before Dobbs singled with one in the seventh for the Marlins' first hit. Eric O'Flaherty relieved Lowe with the bases loaded and Atlanta leading 2-0, and after McCann made nice stops on a couple of pitches in the dirt, Stanton struck out to end the inning.
Schafer led off the game with a single, stole second and scored on a two-out single by McCann. Schafer tripled with two out in the fifth and scored on a single by Alex Gonzalez.
Notes: Braves LF Martin Prado was held out of the starting lineup. He bruised his left knee when hit by a throw stealing second base Tuesday. Manager Fredi Gonzalez said he might miss only one start. ... Marlins SS Hanley Ramirez (strained back) hit in the batting cage and played catch. He may begin a rehabilitation assignment Friday. ... Florida CF Chris Coghlan made a leaping catch to rob Gonzalez of an extra-base hit in the first inning.