Milwaukee scored four times in the ninth inning to down San Diego, 4-2, on Tuesday and the Padres squandered an eighth-inning lead on Wednesday before winning, 8-6.
Brian Lawrence (3-6) held the Brewers at bay for eighth innings on Thursday before the Brewers showed life in the ninth.
Scott Podsednik opened the inning with his third hit of the game, a ground rule double to center field. Lawrence got Richie Sexson on a groundout and struck out Geoff Jenkins before Brady Clark delivered an RBI single to center.
Clark took second on a wild pitch before scoring on a double to left field by Wes Helms to tie the game. Perez followed with a run-scoring single to center field.
The Brewers have scored 37 runs against San Diego this season and 26 have come with two outs.
The Padres scored their runs in the third and sixth.
Lawrence allowed seven hits, walked two and struck out eight to lose for the sixth time in seven decisions.
Brewers starter Matt Kinney hit Brian Buchanan with the bases loaded in the third and Jermaine Clark hit a sacrifice fly three innings later.
Kinney allowed two runs and four hits in 5 2/3 innings.
Leo Estrella (1-0) pitched a scoreless eighth for the win and Mike DeJean worked the ninth for his 10th save.