In December 2003, Pérez signed a contract to return to play for the Braves. He served as a backup catcher to Johnny Estrada in 2004 and 2005. On May 18, 2004, he was the last out of Randy Johnson's perfect game, being called upon to pinch-hit for pitcher Mike Hampton because of excellent career numbers against Johnson (6 hits in 13 at-bats). Nonetheless, he struck out to end the perfect game. He suffered tendinitis in his right shoulder during the 2005 season and was placed on the disabled list for most of the season. While on the disabled list, Perez's duties as catcher were taken over by Brian McCann who eventually took over as the Braves' starting catcher. He returned to make one final major league appearance as a pinch hitter on September 27, at the age of 37.