The Braves opened the final regular-season series two games ahead of San Diego in the NL wild-card race. The Padres played later at NL West-leading San Francisco.
Rollins made his third start since returning from a tight right hamstring. Ryan Howard had two hits, including a two-run single in a four-run eighth. Carlos Ruiz had three hits.
Atlanta has a tribute planned for Cox on Saturday. The Braves are trying to send their longtime manager into retirement with one final postseason appearance.
With Rollins back in the lineup, the NL East champions had 13 hits and looked ready for the postseason.
Trailing 11-2, the Braves tried to rally against left-hander Mike Zagurski in the ninth. Derrek Lee, who had three hits and five RBIs, hit a three-run double to knock Zagurski out of the game.
Right-hander David Herndon walked Melky Cabrera before Matt Diaz grounded out to end it.
Kyle Kendrick (11-10) gave up five hits and two runs in five innings.
Braves rookie Brandon Beachy (0-2) allowed seven hits and four runs, two earned, in 5 2-3 innings in his first home start.
The Braves, who lost three straight games at Philadelphia from Sept. 20-22, took the lopsided loss before a sellout crowd of 51,139.
Atlanta relievers Peter Moylan and Mike Minor issued bases-loaded walks in the sixth and eighth, respectively. The Braves also were hurt by third baseman Brooks Conrad's throwing error with two outs in the sixth.
Conrad made a wild throw to second base after fielding a grounder by Ruiz, leaving the bases loaded. Moylan's walk to pinch-hitter Domonic Brown forced in a run before Rollins hit his third career slam and first of the season.
Raul Ibanez and Ruiz had run-scoring singles off Beachy in the fourth.
Cristhian Martinez gave up three hits and four runs in the eighth. Ben Francisco had a run-scoring single and Chase Utley's bases-loaded walk forced in a run before Howard's two-run single.
Phillies manager Charlie Manuel announced Roy Halladay and Roy Oswalt will start the first two games of the division series.
Manuel did not announce his Game 3 starter. The likely choice is Cole Hamels, who will start the final regular-season game against the Braves on Sunday.
Lee's RBI double drove in Jason Heyward to give Atlanta a 1-0 lead in the first. Lee added a run-scoring single in the fifth.
Some of Cox's former players, including Andres Galarraga and Gerald Perry, arrived on Friday for Saturday's tribute. A huge No. 6 - Cox's uniform number - was cut in the center-field grass.
Notes: Braves president John Schuerholz celebrated his 70th birthday. ... Cox said RHP Jair Jurrjens, who hasn't pitched since Sept. 14 because of an injured right knee, "threw good" in the bullpen but "felt it every now and then." ... Phillies OF Shane Victorino is expected to return Saturday after his wife gave birth to a boy on Thursday. ... 3B Placido Polanco returned to the team after having a cortisone shot in his left elbow Wednesday in Philadelphia.