Jayson Werth and Eric Bruntlett hit solo homers for the Phillies. Mark DeRosa had a disputed solo shot for the Cubs.
Cedeno walked leading off the 10th against Rudy Seanez (0-1) and Geovany Soto walked after Ryan Theriot's sacrifice. Zambrano, a career .215 hitter with 12 homers, was called on to pinch-hit because the Cubs were out of position players.
The left-handed hitting Zambrano bounced a grounder to shortstop Bruntlett that should've been an inning-ending double play. However, first baseman Ryan Howard couldn't scoop Utley's poor throw to first and Cedeno scored.
The Phillies have committed 15 errors, second only to Pittsburgh.
Utley, who has four of the errors, may have rushed his throw because Zambrano busted it down the line.
"Z put the ball in play and he hustled," DeRosa said. "That shows the character of this team."
Zambrano, an 18-game winner last year, took the loss in the series opener on Friday.
Kerry Wood (1-0) pitched two scoreless innings and Bob Howry finished for his first save.
Utley doubled with two outs in the 10th. After Howard was intentionally walked, So Taguchi grounded out to end it.
Playing without shortstop Jimmy Rollins and center fielder Shane Victorino, the defending NL East champions missed a chance to go above .500 for the first time this season.
Rollins wasn't in the starting lineup for the fifth straight game because of a sprained left ankle, but the 2007 NL MVP could return Tuesday. Victorino was placed on the disabled list with a calf injury, forcing manager Charlie Manuel to juggle his lineup. Geoff Jenkins batted leadoff for the first time in his 11-year career and Werth started in center for Victorino.
Manuel earned his first ejection of the season for arguing DeRosa's homer off Jamie Moyer in the sixth that gave Chicago a 4-2 lead. DeRosa hit a high drive down the left-field line leading off the inning.
Third-base umpire Adrian Johnson called it fair, though replays showed the ball was just foul. Left fielder Pat Burrell immediately trotted in to state his case and Manuel ran out to express his opinion.
After the umpires refused to overturn the call following a brief meeting, Manuel continued arguing and was tossed.
"I thought it was foul," Manuel said. "I saw the replay."
Cubs manager Lou Piniella had a different view.
"It looked fair to me," he said.
Told by reporters the ball was foul, Piniella replied: "Really? You mean the umpires were wrong?"
Cubs starter Jason Marquis gave up two runs and four hits in five innings. Marquis turned a two-run lead over to Michael Wuertz, who didn't retire a batter in the sixth.
Bruntlett hit his first homer leading off. Carlos Ruiz and Jenkins followed with singles. Werth then chased Wuertz with an RBI single that tied it at 4. Sean Marshall entered to face Utley, who drove in Jenkins with a sacrifice fly that put the Phillies ahead 5-4.
The Cubs tied it at 5 on pinch-hitter Soto's checked-swing RBI single off J.C. Romero in the eighth. Tom Gordon started the inning but ran into trouble with one out.
Moyer allowed four runs and nine hits in five innings.
"I'm not quite where I want to be," Moyer said. "I'm getting there slowly."
Jenkins was 2-for-6 in his new spot atop the batting order. Jenkins was mostly a middle-of-the-lineup hitter his first 10 seasons with Milwaukee and has hit sixth or seventh with the Phillies. He batted higher than third just twice - both in 1999 - in 1,246 games.
