Howard gave the World Series champion Phillies a 1-0 lead with a homer in the second inning off starter Tommy Hanson (9-3), who was celebrating his 23rd birthday. After Jayson Werth struck out, rain forced a delay of 63 minutes.
Play then resumed for 7 minutes before another 45-minute stoppage.
In the fourth, Howard drove a two-run shot to center off Kris Medlan for his 22nd career multihomer game and fifth this season. The slugger also stroked a double and walked to finish 3 for 3 with three RBIs.
Howard has 11 home runs and 29 RBIs in his last 15 games, with a .339 batting average, and appears to have started his annual late-season surge.
More could be on the way. From Aug. 26 through the end of the past two seasons, Howard has hit a combined .317 with 25 homers and 54 RBIs.
Martinez started for Philadelphia and allowed one hit and one walk in two innings. He was on deck in the second - following the first delay - but didn't return after the second stoppage.
As he did on Aug. 18, Moyer (12-9) relieved Martinez. The 46-year-old lefty worked 4 1-3 innings, allowing one run and four hits with no walks and five strikeouts. It was his second win in relief after being bumped from the rotation.
Ryan Madson loaded the bases in the eighth, but escaped by getting Adam LaRoche on a fly to center field. Struggling closer Brad Lidge, who leads the majors with nine blown saves, worked a quick ninth for his 26th save.
Matt Diaz drove in Atlanta's first run in the fifth with the second of his three doubles. Chipper Jones added an RBI groundout.
NOTES: Phillies reliever J.C. Romero was in Philadelphia to have his strained left forearm examined. There is still no timetable for his return. ... Lidge arrived at Citizens Bank Park with a "military" style haircut, a developing trend among the relievers. ... Matt Stairs pinch hit for Philadelphia in the seventh and grounded out, extending his slump to 0 for 25. His last hit came on July 11. ... Atlanta CF Nate McLouth, who has missed 10 games with a strained left hamstring, went 1 for 2 with a walk while playing center for Double-A Mississippi.