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The Turin club gave their immediate backing to Conte when he decided to appeal against the lengthy suspension, given to him for his alleged failure to report two incidents of match-fixing while in charge of Siena.
But despite Conte appearing in person at the Federal Court of Justice in a bid to have his suspension overturned, the Italian Football Federation (FIGC) upheld original punishment.
In a statement released on Juventus' official website, Agnelli said: "Today's judgment from the Federal Court of Justice confirms the worst suspicions about the Antonio Conte affair, concerning the acts that allegedly occurred when he was working for another club.
"For many months I have observed this situation with disbelief, with a growing sense of bewilderment, as sporting justice started to resemble a witch hunt."
Former Siena player Filippo Carobbio, banned for 26 months for his involvement in the 'Calcioscommesse' scandal, brought Conte to the attention of the authorities by accusing him of instructing his players to draw games against Novara and Albinoleffe in May 2011.
And on revising their original verdict today, the disciplinary commission absolved Conte of all blame for his involvement with the Novara game, but upheld his ban based on their investigation into the events surrounding the Albinoleffe game.
An FIGC statement read: "The Federal Court of Justice can confirm the 10-month disqualification for Antonio Conte.
"It was decided to acquit Conte for his role in the Novara-Siena game, but the 10-month disqualification stands as a disciplinary commission sanction concerning Albinoleffe-Siena."
Agnelli added: "Enough is enough. He was presented with a clear legal victory, namely his acquittal for failing to report on Novara-Siena.
"It was this game that revealed the contradictions and retractions of a 'penitent' seeking only to improve his own situation.
"But the decision was made to ignore logic and apply the penalty in an arbitrary manner, or even to double it.
"In essence, after months and months of hearing from Filippo Carobbio that his coach instructed his players to fix a match during a technical meeting, now they have recognised Antonio Conte's complete innocence in that episode.
"But instead they took refuge in the second accusation (Albinoleffe-Siena) in order to apply the same original sentence."
With Conte's assistant Angelo Alessio also suspended for six months, Massimo Carrera will remain in charge of Juventus as they begin their title defence against Parma on Saturday.
Agnelli also confirmed the club's intention to seek a second appeal through the Italian Olympic Committee (CONI).
He added: "I reiterate my full personal support, and that of Juventus, for Antonio Conte and Angelo Alessio, who are fighting against a system which needs to be rebuilt from its very foundations.
"I am confident that the judicial bodies of CONI will know how to deal with this profound injustice."
Having considered the appeals of 23 individuals and seven clubs in total, the FIGC also upheld the acquittals of Juventus players Leonardo Bonucci and Simone Pepe, and ex-Bari players Nicola Belmonte and Salvatore Masiello.
Marco Di Vaio and Daniele Portanova had each been suspended for six months for their alleged failure to report match-fixing in the Bologna-Bari match of May 2011, but today Di Vaio was acquitted.
Former Siena defender Emanuele Pesoli, who chained himself to the gates of the FIGC for four days in protest against his three-year ban, saw his suspension upheld.
Lecce's demotion to the Lega Pro (third tier) was also confirmed but Grosseto, who had originally been handed the same fate, were spared relegation.
