Zambrano was lifted for a pinch-hitter in the fifth, and Barrett was supposed to stay in the game. But he had gone into the clubhouse and got into another fight with Zambrano there. Barrett was replaced defensively in the sixth by Koyie Hill.
Cubs officials said Barrett was taken to a local hospital. His lip was cut from the clubhouse fight.
It's been a tough week for Barrett, who made several mistakes in Sunday's game in Los Angeles, and was picked off second base on Tuesday in Chicago against the Florida Marlins. Piniella had given Barrett a "mental health" day off Wednesday.
Henry Blanco has been Zambrano's catcher lately, but he was placed on the disabled list Friday because of a herniated disc.
"As an organization, we're very disappointed about the incident today between Michael and Carlos," Cubs assistant general manager Randy Bush said. "They're two highly competitive and caring individuals who put a lot into the game. Frustrations boil over. It can happen. Those of us who have been in the game have seen it happen before.
"We're disappointed, very disappointed," Bush said. "I think it shows the level of frustration among the players, the coaches, the manager. We're not playing as well as we thought we would at this point."
Piniella will handle the disciplinary action, Bush said. If the Cubs manager decides to fine the players, that will be dealt with by team management.
The Braves had taken a 2-0 lead by taking advantage of sloppy play by the Cubs. Atlanta sent nine batters to the plate in the fifth, and opened a 7-1 lead. Zambrano was charged with seven runs, six earned, on 13 hits and two walks over five innings. Atlanta won, 8-5, to hand the Cubs a season-high fifth straight loss. They're now 22-30.
"A lot of the players have expressed they're pressing, they've said that publicly, and a lot of that is probably trying to do too much for the fans here at home," Bush said. "We're disappointed. Lou will address it [Saturday] with the players."
Bush said it isn't the first time he's seen players fight. That doesn't make it right.
"It's unacceptable," Bush said. "Absolutely, it's unacceptable. You never like to see teammates get into it like this."