The club president was left fuming after the appeal against the suspension of the coach was turned down, and called for reforms in the country's legal system
The coach was suspended by the Italian Football Federation (FIGC) until the end of 2012-13 after failing to report two incidences of match-fixing while he was in charge of Siena.
The coach and the club filed an appeal against the decision, but the court refused to remove or reduce the ban.
"For many months I have observed this situation with disbelief, accompanied by a growing bewilderment regarding sporting justice which resembles a witch hunt," Agnelli told the club's official website.
"Given that Conte was found not guilty in one of the two matches for which he was originally sentenced, the decision to uphold the full sentence arbitrarily imposes a sentence that, in effect, is double what it should be.
"To impose the original sentence is like not accounting for the truth, fair justice and fails simple arithmetic. For months, I listened to members of the concerned legal institutions, and other commentators in the field told me to trust the sport judicial system.
"Yet, this is a system content to make decisions and brandish penalties in the absence of evidence. It is a system that allows for plea bargains to be easily lodged, yet, rejects them without reason. "
Despite the outcome, Agnelli once again declared his full support of his coach.
"I reiterate the full support of Juventus towards Antonio Conte as well as Angelo Alessio, who is also fighting against the system which, in my opinion, is in need of great structural reform. Antonio Conte, as already repeatedly stated is and will remain the coach of Juventus
"However, I am confident in the judicial bodies of C.O.N.I, who we will now look to help us in this battle against such profound injustice which among other things causes damages not just to individuals but companies, too."