Bako remained with the Braves for the 2001 season, where he was the backup to Javy López. He batted .212, amassing the third-highest (20) walk total among Atlanta's bench players and batting in 15 runs. His top performances of the season were a 3-for-4 game against the Montréal Expos in August and a 2-for-3 night—with 2 walks—in October against Florida. Bako appeared in three games during the 2001 National League Division Series (NLDS), his first playoff appearances, and three more during the National League Championship Series (NLCS). In Game 3 of the NLDS, Bako went 2-for-2 with a two-run home run in the second inning; he also batted in a third run on a squeeze bunt in the fourth.