Conte had his 10-month suspension for failing to report match-fixing - while in charge of Siena - cut to just four months by TNAS on Friday, meaning he will be back in the dug-out for Juve's trip to Palermo on December 9.
Technical director Massimo Carrera has earned Juve 16 points from the 18 available so far, but Agnelli cannot fathom why Conte has to sit out a further nine Serie A games before his return.
The Juve president told the club's official website: "I maintain my belief, one that is shared by everybody at Juventus, that Antonio Conte is an innocent man.
"The confirmation of his ban is unjust.
"Everyone at Juventus is looking forward to finally having (him) back on the bench, where he can make the most of his talent and continue his work with devotion and dedication.
"Starting today, sporting institutions need to pursue a reform of the justice system in order to avoid a repeat of this situation."
Such issues can not occupy interim boss Carrera, though, as he plots to extend La Vecchia's 45-game unbeaten run at the Stadio Artemio Franchi.
Leonardo Bonucci, who scored an incredible equaliser against Shakhtar Donetsk in midweek, is suspended for picking up his fourth yellow card of the season, allowing Luca Marrone the chance to deputise.
Siena boss Serse Cosmi knows only a flawless performance will do if the Robur are to end Juve's astonishing run.
"We'll need the perfect game to beat them," he said. "They've been in difficulty just twice this season, against Fiorentina and against Shakhtar.
"They only played to 50% of their potential in those games, with their opponents at 90%.
"That means Juventus don't even lose games on an off day.
"We'll have to be at 100% and then we'll see what happens."
Ominously, the Robur have not beaten Juve in Tuscany since May 2008 and they will have to amend that record without midfielder Gaetano D'Agostino, who is training alone in a bid to recover from a muscle injury.