It was a costly defeat for the Dodgers, who slipped 3 1/2 games behind the Florida Marlins in the National League wild card race with seven games remaining. They also trail Philadelphia by 2 1/2 games in that race.
Perez (12-12), who had missed his last start because of a torn fingernail, fell behind 4-0 before retiring a batter. The big hit was a three-run homer by Phil Nevin.
Jackson surrendered two runs in the second and another in the fourth.
Mike Bynum (1-3) allowed three runs and six hits in five innings to pick up the win, just the Padres' fifth in 17 games.