Philadelphia had put runners at the corners with two outs in the top of the seventh before Ryan Howard's hard grounder went off Derrek Lee. The first baseman retrieved the ball and flipped to pitcher Jeff Samardzija for the out, but replays showed Howard beat the throw. Phillies third-base coach Steve Smith was ejected by plate umpire Bill Welke during the ensuing argument.
Samardzija (1-0), a former Notre Dame receiver, got his first major league win. Carlos Marmol struck out two with two on in the eighth and pitched a perfect ninth for his seventh save in nine chances.
Philadelphia, which began the day one game behind the NL East-leading New York Mets, lost its third in a row.
Matched against former Oakland teammate Rich Harden, Phillies starter Joe Blanton held the Cubs hitless until Aramis Ramirez hit a two-out single in the fourth. With a 2-0 lead, he ran into trouble the following inning when Mark DeRosa walked, stole second and moved to third on Henry Blanco's infield single to third.
Pinch-hitter Daryle Ward hit a perfect double play grounder to second with one out but, after taking Chase Utley's toss for the forceout, shortstop Jimmy Rollins sailed a throw over Howard at first as DeRosa scored.
Chicago tied it in the sixth on four walks, three by Blanton and one by former-Cub Scott Eyre to Kosuke Fukudome.
Harden and Blanton were traded within nine days of one another in July and had chatted with each other behind the batting cage on Thursday.
Harden allowed two runs, three hits and four walks in five innings. In his first appearance against the Cubs, Blanton gave up two runs and two hits in 5 2-3 innings.
Pat Burrell hit an RBI single in the first, and the Phillies made it 2-0 in the fifth. Utley singled and raced to third when Howard singled to right, then scored when Fukudome's throw to first apparently hit Howard for an error, and the ball got away from Lee.
Notes: The Phillies were held without an extra-base hit for the first time in 61 games since June 18.