The former Siena boss saw his suspension for failing to report two instances of match-fixing reduced from 10 to four months on Friday, but Agnelli feels Conte should not have been banned at all.
"The confirmation of his suspension is an injustice which should prompt the entire footballing system to ask itself questions," an official statement reads.
"I maintain my view, which is shared by everyone at Juventus, that Antonio Conte is an innocent man and in no way guilty of the charges levelled at him.
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Conte will be able to return to the Juve bench for the clash with Palermo on December 9, one day after his ban expires.