Milwaukee's bullpen couldn't hold the lead in that contest, though, and its late-inning blunders have been a frustrating trend all year.
Lee seeks his first career victory over the slumping Brewers in the opener of a four-game series Thursday night at Miller Park.
Lee (2-7, 3.85 ERA) began his season with 13 consecutive winless outings before beating the Mets on July 4, and things haven't been much better since.
The left-hander allowed four runs and 10 hits - including a three-run homer - in seven innings of a 4-1 loss to St. Louis on Saturday.
Lee, who surrendered three home runs in his previous start, has given up 19 in 140 1-3 innings - one more than he allowed over 232 2-3 frames in 2011. He hasn't yielded this many homers since allowing 29 with Cleveland in 2006.
"I don't know what my home run numbers were or are this year, I just know ... I need to be more down in the zone and induce more ground balls," Lee told the Phillies' official website. "When they're hitting the ball in the air, that's not good for me."
That was especially true the last time he faced the Brewers. Lee tied career highs by allowing 12 hits and four home runs while giving up a season high-tying six runs in seven innings July 24, though Philadelphia rallied to win 7-6 after he'd left the game.
Lee is 0-1 with a 5.54 ERA in four career starts versus Milwaukee. He and Philadelphia (54-63) will both look to get back on track after the Phillies lost 9-2 to Miami on Wednesday. Ty Wigginton homered and had an RBI single, but the Phillies had their three-game winning streak snapped.
Philadelphia won three consecutive 7-6 games in sweeping its series with Milwaukee from July 23-25. The Brewers blew each of their three save opportunities in that series, and Jim Henderson gave up two runs in the ninth to blow another chance in Wednesday's 7-6 loss at Colorado.
Milwaukee (52-64) has lost dropped five of six with the bullpen converting one of three save chances in that stretch, and its 23 blown saves are the most in the majors.
"We play pretty good baseball and then give it up at the end,'' manager Ron Roenicke said.
Ryan Braun, who is hitting .143 over his last 10 games, was held out of the lineup Wednesday at his urging. It's unclear if the slumping slugger will play Thursday as the Brewers look to help Marco Estrada end a nearly year-long winless drought.
Estrada (0-5, 4.36) hasn't won since beating Pittsburgh last Aug. 23. He's gone 14 straight starts and 28 overall appearances without a victory after allowing four runs in four innings of Milwaukee's 6-5, 10-inning loss to Houston on Saturday.
In his only career start against the Phillies, the right-hander allowed five runs and eight hits in four innings of the Brewers' loss in the series finale last month. He has no record, a 7.84 ERA and a blown save in one start and six career relief appearances versus Philadelphia.