Francisco led off the 12th inning with a home run off Cubs closer Kevin Gregg and the Phils won despite getting only three hits all game.
Jimmy Rollins also homered for the Phillies, who won for just the fourth time in 12 games and remained 3.5 games ahead of Florida in the National League East. The Cubs have lost five of six.
Francisco, acquired from Cleveland in the July 29 trade that also included star left-hander Lee, lined a 1-1 pitch from Gregg (4-4) into the basket that hangs over the left-field fence. Francisco is batting .345 with six homers and 12 RBIs in his last 16 games.
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His shot made a winner of Scott Eyre (2-1), who fell out of favor in Chicago last season and was traded to Philadelphia, where he went on to win a World Series ring. After Eyre worked 1.1 perfect innings, Chad Durbin, fresh off the disabled list, pitched a hitless 12th for his second save.
Leading 3-2, the Phillies thought they had scored a ninth-inning insurance run on Carlos Ruiz's homer down the left-field line. But the umpiring crew used replay review and correctly ruled it a foul ball. It was the first video review ever at Wrigley Field.
The Phillies were still ahead when Brad Lidge blew another save. He lost the lead in the bottom of the ninth suffering his seventh blown save in 28 tries after going 41-for-41 last year. Kosuke Fukudome drew a leadoff walk, advanced on Ryan Theriot's sacrifice bunt and scored the tying run on Milton Bradley's line-drive single to right. Lidge has a 7.29 ERA; it was 1.95 in 2008.
Rich Harden dazzled for the Cubs retiring the first 16 batters before walking Ruiz. In sixth with two outs, Rollins broke up the no-hitter with a homer into the right-field bleachers.
J-Roll is batting .325 with eight homers and 27 RBI in 151 at-bats since snapping a career-worst 0-for-28 streak.
Harden allowed only one other hit, Ryan Howard's single, in seven innings.
The Phillies took the lead in the eighth when Carlos Marmol hit a batter and issued three walks, the third to Howard with the bases
loaded. Opponents are batting only .166 against Marmol, but he has walked 52 batters and hit 11 others in 53 2/3 innings.
Philadelphia starter J.A. Happ, who leads the NL with a 1.84 road ERA, allowed seven hits and two runs in six innings.