Atlanta, which began the day four games behind first-place Washington in the NL East, has won five straight.
Tim Hudson (10-4) gave up two runs and seven hits in 5 2-3 innings. Hudson combined with Ben Sheets and Mike Minor to give Braves starters four runs and one walk allowed in the series.
Jonny Venters, Chad Durbin, Eric O'Flaherty and Cristhian Martinez followed with two-hit relief.
With the Braves ahead 3-2, Freddie Freeman hit a two-run single off Jake Diekman in a three-run seventh.
In danger of ending a streak of consecutive playoff appearances at five, Philadelphia (45-57) is last in the NL East this late in a season for the first time since Aug. 12, 2002, according to STATS LLC. The sweep could turn the Phillies into sellers before Tuesday's deadline for trades without waivers. Shane
Victorino, Hunter Pence and Joe Blanton have been mentioned in trade speculation.
Atlanta also swept a three-game series at Philadelphia from July 6-8. The Braves have won six straight over the Phillies for the first time since 1996-97, STATS said.
Halladay (4-6), a two-time Cy Young Award winner, allowed three runs and six hits in six innings with seven strikeouts, dropping to 0-1 with a 5.82 ERA in three starts after missing seven weeks with a strained right lat muscle. He got his 2,000th strikeout in the first inning, fanning David Ross.
Victorino had three hits, including a homer.
Atlanta took a 2-0 lead in the first as five straight hitters reached with two outs. Heyward hit a first-pitch homer, his 16th home run of the season, and Dan Uggla stopped an 0-for-21 slump with an RBI double.
Jones led off the third with his 10th homer, pushing the lead to 3-0. He has 1,042 extra-base hits, passing Pete Rose for sole possession of second place for switch-hitters, behind Eddie Murray's 1,099.
Victorino led off the fourth with his ninth homer and Carlos Ruiz knocked out Hudson with an RBI single in the sixth.
Diekman dropped Heyward's grounder for a run-scoring error in the seventh.
NOTES: Braves manager Fredi Gonzalez expects SS Andrelton Simmons, who was placed on the 15-day DL with a broken right little finger on July 13, to need six weeks to recover, including an injury rehab stint. That would place his return around Aug. 24. ... Laynce Nix made his first start of the season in right field. Hunter Pence, who had started 100 of the first 101 games in right field, remained in right field after his pinch single in the sixth. ... The Phillies are off Monday and open a series at Washington on Tuesday night with LHP Cliff Lee on the mound. Braves RHP Tommy Hanson will face Miami LHP Mark Buehrle in the opener of a four-game series on Monday night.