Mike Cameron also hit a three-run homer off Phillies starter Cliff Lee (7-3), who gave up nine hits in six innings.
After taking Thursday's series opener from the Brewers, the Phillies couldn't make another dent in their magic number of four for clinching the NL East title. Second-place Atlanta won 4-1 at Washington.
Manny Parra (11-10) made his first start since leaving his Sept. 8 outing after one inning because of neck spasms, giving up four hits in seven innings with eight strikeouts.
After the Phillies put their first two runners on in the ninth, Trevor Hoffman came in and retired three straight for his 36th save.
The Phillies remain in good shape to clinch the division, but certainly have a few issues to sort out before they try to defend last year's championship.
General manager Ruben Amaro Jr. said before the game that the team would look at other options for closing games - although he said Brad Lidge, who has a major league-worst 11 blown saves, remains in the mix.
Lidge pitched the seventh against Milwaukee, giving up an RBI single to Casey McGehee.
Also, Pedro Martinez was scratched from Saturday's start because of lingering neck soreness. Right-hander Kyle Kendrick will replace Martinez against the Brewers, and it is not clear when Martinez will pitch again.
Then there's Lee, who was dominant in his first five outings for his new team after he was acquired from Cleveland in July. But Lee now has given up four runs or more in four of his last six starts, including three six-run outings.
Felipe Lopez doubled and scored on Fielder's single in the first. McGehee doubled and Fielder was held up at third. Cameron then drove a 2-2 pitch from Lee deep to left field for his 22nd homer and a 4-0 lead. It was the fifth longball allowed by Lee since the trade.
The Phillies got two runs back in the fourth. Jimmy Rollins reached on an error by third baseman McGehee and Shane Victorino walked to set up Howard's sharp two-run single off first baseman Fielder's glove.
Milwaukee then took a 7-2 lead in the fifth, when Fielder smacked a 2-0 pitch from Lee into the second deck in right field with Ryan Braun and Corey Hart on base.
NOTES: Amaro said LHP J.C. Romero and RHP Brett Myers could be ninth-inning options for the Phillies. The team hopes both will return from injuries next week. ... Howard's two-run single in the fourth originally was ruled an error by Fielder, but the official scorer reversed the decision one inning later.