The collapse is complete as Atlanta lost, 4-3, in 13 innings to Philadelphia on the final day of the season to miss the playoffs.
The Braves (89-73) had a 10 1/2-game lead in the National League wild card race on August 25, but went 10-20 down the stretch and lost their final five games of the season as the Cardinals snuck into the playoffs by beating Houston on Wednesday.
The Phillies (102-60), meanwhile, set a franchise record for most wins in a season and manager Charlie Manuel also set a franchise record for most wins for a Phillies skipper with his 646th victory.
Philadelphia, which will have home field advantage throughout the playoffs, will host St. Louis on Saturday for Game 1 of the National League Division Series.
"They're a good team, they can hit," Manuel said of the Cardinals. "They were a challenge for us. At the same time I look at it, they've got good hitters but they can be a little weak on defense. But they've got talent in their bullpen. They've got big arms."
Justin De Fratus (1-0) got the first win of his career for pitching a scoreless 12th inning while Hunter Pence drove in the game-winning run for the Phillies, who won their final four games of the season after dropping a season-high eight straight games.
After De Fratus got Martin Prado to groundout with two outs and a man on third in the 12th, Brian Schneider worked a one-out walk off of Scott Linebrink (4-4) in the 13th, but Jimmy Rollins then flied out. Chase Utley, though, kept the inning alive with a single to right. Pence then dropped a bloop single in the infield near first and Schneider scored for the lead.
"That's a good ball club over there, but I'm really proud of our club, the way we battled," Braves manager Fredi Gonzalez said. "We had an opportunity to play for tomorrow and we didn't capitalize on that. But again, a lot of good stuff this year and maybe we'll be better off for it next year."
The Phils struck in the first inning when Pence worked a two-out walk and Ryan Howard followed with a double into the corner in left for an early 1-0 advantage.
The Braves used the speed of Bourn to tie the game in the bottom of the first as he led off with a single, stole second, moved to third on a groundout and came home thanks to a sac fly from Chipper Jones.
After leaving runners at the corners in the second, Atlanta went ahead in the third. Bourn led off with a single and Prado later singled. After Bourn was caught stealing third, Jones struck out, but Uggla hit an 0-2 pitch over the left field wall for a 3-1 advantage.
The Phillies put their first two men on base in the fourth, but were unable to plate any as Hudson got John Mayberry to hit into a fielder's choice, Raul Ibanez to strike out and Placido Polanco to ground out and end the frame.
Atlanta threatened in the sixth when it put its first two batters on base with walks off of Vance Worley, who then struck out the next two batters. Jack Wilson then punched a single into right, but Pence fielded it on one hop and threw a strike to home, with Carlos Ruiz applying the tag to Uggla for the third out of the inning.
The Phils cut into their deficit in the seventh. With one out, Ibanez doubled and Polanco followed with a single. Ruiz then reached base on an error from Wilson and Ibanez scored to make it a one-run game.
The Phils had recorded 101 wins in 1976 and 1977..Manuel passed Gene Mauch, who skippered the Phils from early in the 1960 season until being relieved of duties during the 1968 season...The Phillies took 12 of 18 from the Braves this season, including the final seven games...The Phillies batted just 2- for-12 with runners in scoring position and stranded 15...Joe Blanton started the game for Philadelphia, but was pulled after two innings as he gave up a run on three hits.