Baez had walked with one out in the second inning and tried to steal second, appearing to hit his head on second baseman Ozzie Albies' knee. Baez was called out, but the Cubs challenged the call, which stood after a review.
Baez took the field for the Braves' third, but after one batter, athletic trainer PJ Mainville went out to check on the shortstop, who was then lifted from the game.
He was taken to Northwestern Memorial Hospital to be evaluated. A team spokesman said the initial tests were positive and that Baez was not in concussion protocol.
When Maddon first went to check on Baez after the slide, the shortstop said he was OK.
"I put my hand on his shoulder and said, 'Are you all right? Can you stay in?' and he said 'Yes, I'm fine,'" Maddon said.
Maddon was watching the Braves bat in the third and pitcher John Lackey, who was in the dugout, told the manager to check on Baez.
"Lackey said, 'Joe, heads up -- Javy,'" Maddon said. "That's the first time I was aware."
Baez was expected to stay in Chicago overnight Sunday and join the team Monday in Pittsburgh for the start of a four-game series against the Pirates.
"Javy's one of the best shortstops in the league, hands down," Cubs pitcher Mike Montgomery said. "It's unfortunate he came out like that. I hope he'll be all right. We need him. He's a big part of this offense and defense. Hopefully, he'll be all right and be back in there shortly.'"
Mike Freeman, promoted from Triple-A Iowa on Friday, took over at shortstop. The Cubs are thin there with Russell being sidelined since Aug. 3 with a right foot strain. Russell aggravated his injury last week, and was expected to be sidelined three more weeks. Baez doubled and homered Saturday and was batting .271.
"I saw the play where he slid in and then he came back in and said he was OK," Freeman said. "I was walking back in the tunnel and somebody said, 'You're in the game.'
"If anything, maybe it's good to give him a break," Freeman said of Baez. "I know he's been playing his tail off for a while. ... You can't replace Javy Baez and I'm not going to try. Hopefully, he's OK. It's all about winning and I want to win as much as anybody. He's a guy this team needs to win down the stretch. I'm certainly rooting for him."
Maddon said Ben Zobrist may get some work at shortstop.
"I was looking for a day off for Javy and maybe this happened in a bizarre way and got him off his feet," Maddon said.