Tim Hudson and the Braves took a six-run lead, then held on for an 8-7 victory over the Philadelphia Phillies on Sunday.
After beating the Phillies, the Braves watched on TV in their clubhouse as San Francisco beat San Diego 3-0, giving the Braves the NL wild card by one game over San Diego.
Atlanta will start the playoffs Thursday at NL West champion San Francisco in the opener of a best-of-five series.
The Braves won 14 consecutive division titles with Cox but had missed the playoffs since 2005.
There was a postgame REO Speedwagon concert at Turner Field, and a few hundred fans remained after the concert to watch the Giants' win on the video board. They chanted and cheered after the final out as bubbly was sprayed in the Braves' clubhouse.
The fans began chanting "Bobby! Bobby!" while watching the celebration begin.
Cox had compliments for his team.
"We try hard," said Cox, who is retiring after this season. "This team is the hardest-working, hardest-trying team we've ever had here."
Hudson (17-9) allowed four runs and two hits in seven innings against the NL East champions, giving up two-run homers by John Mayberry in the third and Jayson Werth in the seventh.
Billy Wagner struggled in the Phillies' three-run eighth but recovered with a perfect ninth.
"It's a relief because you get a tomorrow," Wagner said. "We knew we had to win the game. We knew what was at stake."
Omar Infante and embattled infielder Brooks Conrad each had two hits and drove in two runs for Atlanta, and Derrek Lee homered.
"The bats came alive, which was great to see," Cox said. "We had much better hitting than we've had lately."
Cole Hamels started for the Phillies, and Roy Oswalt relieved him in the third.
Hudson left with an 8-4 lead. The Phillies scored three runs off Jonny Venters and Wagner in the eighth.
After allowing an RBI single by Wilson Valdez and pinch-hitter Ben Francisco's two-run double, Wagner struck out Raul Ibanez to strand runners on second and third.
Wagner, who like Cox is retiring after the season, struck out Shane Victorino, Brian Schneider and Greg Dobbs in the ninth for his 37th save in 44 chances.
"The shadows helped, no doubt," Wagner said. "They could see fastballs but they couldn't see the spin of breaking balls."
Braves fans in the sellout crowd began chanting "Bobby! Bobby!" after the final out.
Attendance at Turner Field was 52,613 for an Atlanta-record three-game total of 158,048. Atlanta's previous best attendance total for a three-game series was 150,095 for a visit from the Cardinals in 1998.