However, he has been passed fit to play and starts the game, with Tite only making one change from the team that drew 1-1 with Switzerland.
The only change comes at right-back, with Fagner replacing Danilo, who has sustained a muscle injury.
"Danilo will begin treatment with the physiotherapists and will continue under the observation of the medical department," the CBF said.
Corinthians defender Fagner, who made his international debut in 2017, will win his fifth Brazil cap against Costa Rica.
Manchester City striker Gabriel Jesus plays up front, despite drawing a blank against Switzerland, while Philippe Coutinho will hope to build on his exceptional performance last time out, in which he scored a stunning goal. Miranda and Thiago Silva are the centre-backs, with Alisson in goal.
The game takes on added importance following Brazil's slip in their first match, with Serbia currently top of Group E.
Serbia beat Costa Rica 1-0 in their opening game, and face the Swiss on Friday evening.
Brazil team: Alisson; Fagner, Miranda, Thiago Silva, Marcelo; Casemiro, Paulinho; Willian, Coutinho, Neymar; Jesus.
Costa Rica team: Navas; Acosta, Gonzalez, Duarte, Oviedo; Gamboa, Borges, Ruiz, Guzman; Venegas, Urena.