The Juventus defender will not have recovered from his ankle injury in time to take part in Thursday's friendly encounter.
The Juventus defender picked up an ankle knock in his side's 2-0 win over Bologna at the weekend, and will not be recovered in time for the game versus the 2014 World Cup host.
"We conducted new tests on Chiellini's condition this morning and, although recent therapy has improved his condition, I can say with certainty he will not be available for the Brazil game," national team doctor Enrico Castellacci told the official FIGC website.
"The player is also in doubt for the Malta game."
Italy takes on Brazil in Geneva on Thursday, before the World Cup qualifier against Malta on March 26.