Italy coach Roberto Donadoni instead opted to partner Christian Panucci and Giorgio Chiellini at centre-half, moving Gianluca Zambrotta from left-back to right-back and starting Fabio Grosso at left-back.
"The player has expressed a desire to stay with the squad but in the coming days he will have an operation," the statement added.
The Italians were already without captain and centre-half Fabio Cannavaro, who was ruled out of the tournament after rupturing ankle ligaments before the first group game.
Barzagli, who is in the process of moving from Palermo to VfL Wolfsburg in Germany, can not be replaced in the middle of the tournament, leaving Donadoni with limited options.
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