The 28-year-old suffered an ankle injury during Juventus' 2-0 Serie A win at Bologna on Saturday and has not recovered in time to face the five-times world champions in Geneva.
"We conducted new tests on Chiellini this morning and, although recent therapy has improved his condition, I can say with certainty he will not be available for the Brazil game," team doctor Enrico Castellacci said on the Italian Federation's website.
"The player is also borderline for the Malta game."
Italy who are top of Group B with 10 points from four games, play winless Malta in Valletta on Tuesday.
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