Pérez had his best year in 1998 when he posted a .336 batting average along with a .404 on-base percentage in 61 games. He committed only 1 error in 305 total chances for a .997 fielding percentage. His working relationship with Maddux continued to improve with Maddux leading the National League with 5 shutouts, and a 2.22 earned run average. The Braves once again claimed the National League East Division crown and defeated the Chicago Cubs in three games in the 1998 National League Division Series. Pérez hit an eighth-inning grand slam home run in the decisive Game 3 of the series. However, the Braves' season ended when they lost to the San Diego Padres in the 1998 National League Championship Series.