Raul Ibanez and Chase Utley hit solo homers for the surging Phils, winners of nine of 12.
The 47-year-old Moyer (5-2) continued his dazzling start, only struggling briefly when Prince Fielder, Jim Edmonds and George Kottaras all hit solo homers in the second to tie the game.
But Ibanez hit his homer and Shane Victorino drove in two with a triple in the fourth off Randy Wolf (3-3) to give the Phillies a 6-3 lead. Milwaukee cut it to 8-5 with two runs in the seventh, but Utley's solo homer in the ninth sealed it.
Philadelphia wore out its welcome in Colorado against the Rockies earlier this week after allegations of sign stealing when their bullpen coach was caught by TV cameras using binoculars. The issue dominated the stay that included two rainouts.
But there's no place for visitors like Miller Park this season, where the Brewers are used to being hospitable hosts. Milwaukee, wearing its 1970s retro uniforms, fell to a majors-worst 4-12 at home.
Moyer followed up his shutout last Friday by holding Milwaukee's inconsistent offense to five runs.
Fielder hit a 462-foot blast and Edmonds and Kottaras added homers in the second, only the second time in the left-hander's career he'd allowed three homers in an inning, according to STATS LLC.
Moyer went on to win that start on Sept. 9, 2007 against the Marlins. Milwaukee's sputtering offense that scores in bunches or not at all never figured him out again until chasing him with a single and two walks in the seventh.
Reliever David Herndon got a ground ball that could've been an inning-ending double play, but Utley's throw from second was wide right, allowing two runs to score to make it 8-5.
Wolf's solid start since signing a $29.75 million, three-year deal has turned into a miserable May. He's given up five homers and 13 runs over 16 innings in three starts this month.
Howard had been 1 of 9 against Wolf before his two-out homer in the first inning made it 2-0, and Wilson Valdez's RBI double in the second gave Philadelphia a 3-0 lead.
In the sixth, the Phillies turned two errors by reliever Manny Parra into two more runs to go up 8-3 on a run-scoring single by Victorino and a sacrifice fly by Placido Polanco.
NOTES: Milwaukee is 3-19 when scoring five runs or less. ... Phillies C Carlos Ruiz (right knee) was available only in an emergency. ... Brewers LF Ryan Braun (left elbow) returned to the lineup. ... Brewers Hall of Fame broadcaster Bob Uecker says he hopes to be back in the booth for home games sometime in June after heart surgery. ... Tests on Phillies closer Brad Lidge (right elbow inflammation) showed no structural damage to the surgically repaired joint.
