The Phillies got a solid start from Kyle Kendrick (8-3), who pitched into the seventh to pick up the win. Kendrick allowed three runs on seven hits and a pair of walks in six innings plus.
Morton (1-2) could not escape a four-run fourth inning by the Phillies, highlighted by a two-run homer off the bat of Shane Victorino. Run-scoring singles by Ryan Howard and Geoff Jenkins spelled the end of the day for Morton, who lasted just two innings and allowed five earned runs.
The Braves' offense finally went to work in the seventh, scoring three times to make it a 5-3 game. Philadelphia would take those three back in the ninth, tacking on three of their own off Blaine Boyer.
Jones' return went without incident. Around an hour before game time, Braves manager Bobby Cox revised his line-up and added Jones to his familiar number three spot. Jones went 1-for-3 with a walk.
After a back strain kept him sidelined for 33 games, Kotsay went 0-for-4 in his first action since May 25. His return shifted the suddenly surging Gregor Blanco to the starting duties in left field.
Victorino lead the Phillies offensive with a four-RBI night, including his third homer of the season. Philadelphia has now won four straight games against Atlanta at Turner Field, and improved to 6-1 against the Braves this season.
The Braves now trail the Phillies by five full games in the standings, with the Marlins and Mets between them.