Perez got the Brewers' comeback started with a three-run homer off Juan Cruz (1-1) in the eighth inning. After John Vander Wal singled home the go-ahead run in the ninth off Mike Remlinger, Perez followed with an RBI single to make it 8-6. Royce Clayton knocked in the final run on a groundout.
The Brewers won 10 games against the Cubs last season, the most they had against any club in a 106-loss campaign. They have won the first two games between the clubs this year.
Curtis Leskanic (2-0) pitched a perfect eighth inning to notch the victory.
Mike DeJean threw one pitch to Alex Gonzalez in the ninth before the game was delayed 15 minutes by a problem with the lights.
Once the game resumed, DeJean got Gonzalez to fly to right, then finished the inning with little difficulty to pick up his seventh save.
After several balls early in the game died at the warning track, Corey Patterson's three-run blast off Wayne Franklin in the fourth inning made it into the seats in right field put the Cubs up, 4-3.
The Cubs tacked on runs in the fifth and seventh inning, and seemed to be sailing smoothly until the home run by Perez.
Franklin gave up five runs and six hits in 4 2/3 innings. He struck out three and walked one.