In 1999, Pérez was thrust into a starting role when Javy López suffered an injury to a ligament in his right knee in late July and was lost for the season. He stepped in with a .249 batting average along with 7 home runs, 30 runs batted in, and finished fourth in the league in fielding percentage and in range factor. The Braves won their fifth consecutive National League East Division title and then defeated the Houston Astros in four games in the 1999 National League Division Series.