After trailing the Mets by 3½ games going into last Thursday, Philadelphia leads the division for the first time since Aug. 26.
The Phillies led this one 3-0 and 4-3 before the Braves took a 7-4 advantage with a four-run sixth.
Howard had a run-scoring triple as the Phillies scored twice in the seventh.
Lidge walked Chipper Jones to open the ninth, then walked Casey Kotchman and Jeff Francoeur to load the bases with two outs. But the All-Star closer struck out Gregor Blanco, making him perfect in 37 save chances during his first season with Philadelphia.
The Phillies improved to 71-0 when leading after eight innings. They are 7-0 at Turner Field this year and 11-2 overall against the Braves.
Julian Tavarez walked Jayson Werth with two outs in the eighth. Braves manager Bobby Cox brought in Mike Gonzalez (0-3), who gave up Howard's opposite-field homer to left. It was Gonzalez's second blown save in 13 chances.
Making a late push for NL MVP despite a .249 batting average, Howard leads the majors with 45 homers and 136 RBIs. He was 4-for-5 with three RBIs.
Ryan Madson (4-2) had three strikeouts in two perfect innings.
Jamie Moyer gave up six hits and six runs in 5 2-3 innings. He walked four batters, including back-to-back walks to Brent Lillibridge and Greg Norton to load the bases in the Braves' big sixth inning.
Josh Anderson tied the game with a groundout. Kelly Johnson's pinch-hit single off Chad Durbin drove in two runs to extend his career-best hitting streak to 14 games. Brian McCann added a run-scoring single off Scott Eyre for a 7-4 lead.
Werth, who hit a two-run homer, and Shane Victorino each had three hits.
Carlos Ruiz hit a homer off Braves rookie James Parr, who gave up 10 hits and four runs in 4 1-3 innings.
Howard drove in Werth with a seventh-inning triple off Will Ohman. Victorino drove in Howard with a single off Jeff Bennett to cut the lead to 7-6.
Jimmy Rollins' third-inning double set up a three-run third inning. Chase Utley followed with another double to left-center, driving in Rollins. Werth's two-run homer to left gave the Phillies a 3-0 lead.
The Braves tied it in the third. With one out, Moyer hit Anderson with a pitch and walked Martin Prado. Jones' single loaded the bases. McCann drove in Anderson with a single. With two outs, Casey Kotchman hit a two-run single. Jones scored the tying run on a slide that beat Shane Victorino's throw from center.
Ruiz gave the Phillies a 4-3 lead with his homer in the fourth.
Notes: Phillies manager Charlie Manuel said rookie LHP J.A. Happ will replace RHP Kyle Kendrick as Wednesday night's starter against the Braves. Happ, who will be making his third start, has never faced the Braves. ... Braves SS Yunel Escobar missed his third straight start with a strained right hamstring. "We keep saying it's day-to-day, but I think it's a little worse than that," Cox said.