Siena will start the Serie A season with a six-point deduction after their plea bargain was accepted at the second attempt by the FIGC's tribunal over the same case. They must also a pay a 100,000 euros fine.
Promoted Torino were docked one point in Serie A while Varese were deducted one point in Serie B as the tribunal handed out further punishments in the latest scandal to hit Italian football.
Conte, who led Juventus to the Serie A title last season, is accused of failing to report match-fixing in two games in the 2010/11 season when he was coach of Siena, then in Serie B.
Conte, who originally denied all the allegations, changed strategy in recent weeks and tried to reach a deal with federation prosecutor Stefano Palazzi under which he would accept a three-month ban and avoid going to court.
However, the tribunal ruled after a hearing on Wednesday that the proposal agreed with Palazzi, which would have allowed Conte to return to Juventus's bench in November, was not acceptable.
Juventus reacted angrily to the decision.
"Juventus today is imposing a media silence," read a statement on the club's website.
"Tomorrow morning, the situation will be evaluated regarding the events of today which are to be considering, whatever the outcome of this matter, to be a serious act against the good repute of all those involved: professionals, the manager, members and club."
The matches involved in the charges were between Novara and Siena in May 2011, which finished 2-2, and Albinoleffe and Siena in the same month which ended in a 1-0 defeat for Siena.
In total, 13 clubs and 45 players and training staff are facing disciplinary charges over the match-fixing allegations.
The "Calcioscommesse" scandal echoes earlier match-fixing cases which tarnished Italian football in the 1980s and before the 2006 World Cup.
Prosecutors believe an international gambling ring paid players to throw matches in the latest scandal. Dozens of current and former players in teams ranging from the Serie A top division down to the lower leagues may have been involved, according to investigators.
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