The 33-year-old said a penalty decision awarded to Milan in their 2-1 win over Siena on the final day of last season, which ensured they qualified for the competition ahead of Fiorentina, had turned his side into a "joke".
Milan had been 1-0 down in the match and needed two late goals to ensure they finished above Fiorentina, who beat Pescara 5-1.
At the time, a number of players and officials from Fiorentina complained about the penalty decision and Pizarro recently told Corriere dello Sport that "they didn't let us play in the Champions League even though we deserved it".
The Italian Football Federation (FIGC) have now confirmed that both Pizarro and the club are to be investigated over the comments.
"The federal prosecutor has referred Fiorentina player David Pizarro to the national disciplinary commission," read a statement on the FIGC's official website.
"In statements published on the websites of the Gazzetta dello Sport and the Corriere dello Sport on July 22, he publicly expressed opinions and remarks likely to infringe on the prestige, reputation and credibility of the Federation, casting doubts on the neutrality of the institution itself, the fairness of the games and the championship and the objectivity and the impartiality of the referees.
"For their objective liability, (Fiorentina) have also been referred."
In his interview with the Italian newspaper, Pizarro also suggested he had witnessed similar practices at one of his former clubs, Roma.
"I am protesting about a system that allows these kind of things to happen," he said. "The same things I saw at Roma. It's a shame to work hard all week only to be frustrated every Sunday."
