Richarlison is being kept in isolation due to the contagious nature of the illness, with Brazil stating he needs "full rest and medication" in order to recover.
The rest of the Selecao squad will be vaccinated following the match with Paraguay in Porto Alegre.
Brazil were already missing Casemiro through suspension and Fernandinho due to injury, with Tite confirming Allan will therefore start in midfield, potentially alongside Barcelona man Arthur.
"Confirming Allan before the game is to give him confidence," Tite told his pre-match news conference. "It is for him to know that the coach has no doubt.
"If it was another player, like Dani Alves, for example, or Thiago Silva, it would be different. But in Allan's case, he's going to play.”
Brazil have been perhaps the most impressive side at this year’s tournament, having performed admirably in two of their group games.
As for Paraguay, they limped across the line in the group stages and qualified without winning a single game.
Neither Paraguay nor Brazil have won the Copa America in the last decade, with Brazil last tasting success in 2007.
That remains the Selecao’s last major silverware and pressure has grown on them to win this year’s South American championship on home soil.
They will kick-off the quarter-final fixtures when they meet Paraguay on Thursday, before Venezuela face Argentina the following day. Colombia's match with Chile and Uruguay's clash with Peru are the other two games in the last-eight stage.