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Miguel Tejada homered to extend his hitting streak to 18 games and Lance Berkman had a two-run double for the Astros.
Lee (7-4), a strong candidate to start Game 1 in the best-of-five division series Wednesday, worked 5 2-3 innings. The 2008 AL Cy Young Award winner allowed four runs - three earned - and seven hits while striking out six.
Since going 5-0 with a 0.68 ERA in his first five starts with the Phillies, the left-hander is 2-4 with a 6.13 ERA in his past seven. Lee, who extended his career-high innings total to 231, was acquired from Cleveland in late July.
The Phillies enter the final weekend of the season at 92-67, one game behind the Dodgers in the race for best record and home-field advantage throughout the NL playoffs. Los Angeles owns the tiebreaker after winning the season series 4-3.
Philadelphia hosts the Florida Marlins in its last three games. The Dodgers are home against Colorado, which clinched a playoff spot earlier Thursday. The Rockies could still catch Los Angeles for the NL West title with a three-game sweep.
The 70th sellout crowd of the season at Citizens Bank Park greeted Phillies players with a standing ovation, thanking them for winning their third straight division title, which was wrapped up with a 10-3 win over Houston on Wednesday night. Fans received white rally towels that read "National League East Champions, 2009," and they frequently punctuated a festive atmosphere by waving them.
By drawing 44,905 fans, the Phillies set a franchise record for attendance at 3,465,206. The previous mark was 3,422,583, during last season's run to the World Series championship.
Though manager Charlie Manuel said the Phillies would love to enjoy home-field advantage in the playoffs, he also wants his team as healthy as possible. He rested regulars Chase Utley and Shane Victorino on Thursday night and will likely spell Raul Ibanez, Ryan Howard, Jimmy Rollins and Jayson Werth at some point this weekend.
Tejada homered to left in the sixth inning and later singled in a run, leaving him four hits from his fourth 200-hit season. His homer put the Astros further in front after the Phillies cut the deficit to 2-1 in the fifth. Tejada has batted .429 during the streak.
Houston starter Felipe Paulino snapped his seven-game losing streak with five strong innings, earning his first win since June 27. Though he needed 110 pitches, he allowed only one run and six hits.
Jose Valverde yielded two ninth-inning runs but with two on he retired Miguel Cairo on a liner to center field for the final out.
NOTES: Phillies reliever Chan Ho Park returned to Philadelphia after feeling discomfort in his right hamstring during a rehab outing in the Florida Instructional League. He will see team doctor Michael Ciccotti on Friday. ... Astros left fielder Carlos Lee missed the game with a sore right hand.