The Brewers shortstop fell to the ground bleeding and was helped into the locker room by three people. He suffered a gash that required stitches to close.
"I saw the whole thing, so obviously you never want to see a teammate get hurt, especially like that," Brewers starter Marco Estrada said. "It was pretty tough. Once I found out he was doing OK, I kind of focused back on the game. You still have to play."
Braun was swinging a bat on the top step, his usual routine before his first plate appearance, when his bat hit Segura.
"I know after being with him so long that when he's up there with a weight in his hand, you just move out of the way," Milwaukee manager Ron Roenicke said. He said Segura was trying to get into the on-deck circle "in a hurry" when he was hit by the bat.
"[Braun's] been doing it, that's why he goes up to the top step where he can try to get away from people," Roenicke said. "Everybody knows. It's just certain guys have different routines, and you hope everybody's aware of it."
Braun was remorseful when speaking in the locker room after the game.
"You never want to see something like that, you know?" Braun said. "It breaks your heart a little bit, and obviously it's never something that's done intentionally.
"Whenever you're involved in a situation like that, I think it puts life in perspective and you realize how insignificant baseball is," he said. "Thank God we heard he's OK. It could have been a lot worse or a lot worse places he could have been hit."
Roenicke said Segura likely would miss two or three games until the swelling subsides in his face, and he's also listed as day to day.
"It's always hard when you see one of your regulars go down like that," Roenicke said. "It bugged me all game. It's just one of those things you hope you can prevent."
Roenicke said he himself broke two ribs when a teammate struck him with a bat in the on-deck circle while he was in a Triple-A game during his playing career.
"Same thing, guy on deck and didn't see me and swung and cracked two ribs," he said. "It does happen."
The only damage allowed by Estrada (2-1) was a third-inning home run to Luis Valbuena and a two-run homer by Welington Castillo in the eighth.
"What made him really good ... he could throw his offspeed [pitches] when he was behind in the count," Castillo said. "He has a really good changeup."
The right-hander allowed the three runs while striking out nine and didn't walk a batter in 7 2/3 innings.
"That's the best I've felt so far since Spring Training," Estrada said. "I was feeling really good during Spring Training. The last couple games, I just haven't felt like myself, but today I did."
Khris Davis hit his third home run for Milwaukee, a solo shot in the sixth, to give the Brewers a 5-1 lead. Jeff Bianchi, who replaced Segura at shortstop, had two singles and two RBIs.
Francisco Rodriguez pitched the ninth inning for his 11th save in 11 chances. It was his 315th career save, moving him past Robb Nen into 18th place on the all-time saves list. It also topped a franchise record for saves in March/April, set by Francisco Cordero when he posted 10 saves in 2007.
The Brewers have won seven of their last eight games to maintain a Majors-best 18-6 record, while the Cubs have lost four consecutive games.
Milwaukee made it 1-0 in the first off Travis Wood (1-3), when Aramis Ramirez's sacrifice fly scored Carlos Gomez. Bianchi's single scored two more runs in the second to make it 3-0. Gomez had an RBI fielder's choice in the fourth to score Mark Reynolds and give the Brewers a 4-0 lead.