The football federation disciplinary commission acquitted the pair, as well as other players, on Friday after ruling that evidence submitted regarding an alleged attempt to fix a match between Bari and Udinese in 2010 was inconsistent.
Bonucci was playing for Bari at the time, and Pepe for Udinese. The match ended 3-3.
Prosecutor Stefano Palazzi, who has asked for Bonucci to be banned for three-and-a-half years and Pepe for a year, has asked the Federal Court of Justice to reverse the decision, officials said.
The two players would have to prepare a defence before Monday, when the Federal Court would convene to consider the appeal, reports said.