He led the San Francisco Giants in 2002 to the World Series against the Anaheim Angels. During the seventh inning of Game Five, his then-three year old son Darren ran onto the field to retrieve a bat at home plate. He was pulled out of the way by J.T. Snow just before David Bell nearly ran him over as he was about to score. Baker claimed he was too busy managing the game - a 16-4 blowout - to notice Darren had left the dugout. Major League Baseball already had a directive limiting teams to two bat boys, a rule the Giants violated repeatedly during that post-season. In response to the near-tragedy, it implemented the "Darren Baker Rule" which now requires that all bat boys be at least 14 years old.

Baker guided the Chicago Cubs to the NLCS in 2003. Championship-starved Cubs fans immediately embraced Baker, and the shirts bearing the slogan "IN DUSTY WE TRUSTY" became best-sellers throughout the 2003 season. The Cubs came within five outs of reaching the Series before losing to the Florida Marlins in seven games, following the Steve Bartman incident in Game Six; Baker would have become the first manager to lead different teams to the World Series in consecutive years. Although he faced increasing media and fan criticism during and following the disappointing 2004 and 2005 seasons, as of February 2006, he remains manager of the Cubs.

Baker also had an illustrious career as an outfielder for the Atlanta Braves, Los Angeles Dodgers, San Francisco Giants, and Oakland A's from 1968 to 1986, winning a World Series as a player with the Dodgers in 1981. Baker was on deck when Hank Aaron hit his 715th home run, breaking the record previously held by Babe Ruth.