Serie A's disciplinary tribunal banned Chiellini for three games on Monday, saying in a statement that he had been guilty of elbowing Roma's Miralem Pjanic in an off-the-ball incident during Juve's 1-0 win on Sunday.
The tribunal used video evidence to make the decision as the incident was not seen by the referee.
Chiellini is a linchpin of the Italy side but will now have to wait to see if the incident will affect his World Cup chances, with Tuesday the deadline for provisional squads for June and July's tournament in Brazil.
Prandelli, who has largely succeeded in removing the perceived histrionics and negativity from the Italy team, has dropped a number of players for similar incidents in club games since taking over in 2010.
However, Prandelli appeared to indicate that Chiellini would be let off the hook.
"I've seen and reviewed Chiellini's action and for me, it was not a violent gesture," he told the ANSA news agency. "Do I expect to be criticised for this? The four years in which the code of ethics has been in effect have all been controversial."
Roma striker Mattia Destro, banned for four matches for elbowing an opponent in April, was the latest victim of Prandelli's rules when he missed out on two days of Italy fitness tests in April.
Prandelli warned at the time: "Anyone who messes around will stay at home, because it will mean that they can't handle the pressure of a World Cup."
Centre-back Chiellini has been the mainstay of the Italy defence since Fabio Cannavaro quit international football after the 2010 World Cup and has won many admirers at home and abroad for his never-say-die attitude.
Italy are in World Cup Group D alongside England, Uruguay and Costa Rica.
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- Miralem Pjanic