Baker was awarded a double and the Cubs scored the first run on an RBI groundout by Ian Stewart.
Pence said he didn't get the right read on the ball.
During Friday's 5-1 loss to the Cubs, Reed Johnson was credited with an RBI triple after Pence failed to make a sliding catch. In a 6-1 loss to San Diego on April 22, he unsuccessfully dove for a ball and gave Nick Hundley a triple.
"He has been making mistakes in the outfield," manager Charlie Manuel said.
Pence, always a standup person, addressed the issue.
"I got to get better, I guess," he said. "I have to continue to work every day."
Even though he leads the team with 11 RBIs, Pence has struggled recently at the plate, hitting .171 (7 for 41) in his last 10 games.
Catcher Carlos Ruiz, who took a foul ball off his knee Saturday but remained in the game, didn't play Sunday, but said he was feeling fine.
Jim Thome, who left Saturday's game with back tightness, said "It's no worse, and about the same as [Saturday]."
Cubs righthander Matt Garza made quite an impression on the Phillies by striking out 10, walking one, and issuing just one hit in seven shutout innings Sunday.
"Usually he gets a little wild, but he was right around the plate and controlled three pitches and was on today," Phillies leftfielder Juan Pierre said.
Contact Marc Narducci
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