Croatia is charged with "improper conduct" of supporters, including "racist chants, racist symbols" at a game in Poznan on Thursday, UEFA said in a statement.
UEFA received reports from anti-discrimination monitors working with Football Against Racism in Europe, who wrote that Croatia fans made monkey noises and displayed far-right nationalist flags.
Balotelli, who is black, started the game for Italy against Croatia, and was replaced in the second half of the 1-1 draw.
"It was fairly consistent throughout the game," FARE executive director Piara Powar told The Associated Press. "It was at its most intense as he was substituted and left the field."
The charge also relates to fireworks thrown on the field after Croatia scored, which delayed Italy's kickoff to restart the game.
UEFA said its disciplinary panel will judge the case against Croatia on Tuesday.
UEFA rules make national associations responsible for their fans' behaviour. Punishments range from warnings and a sliding scale of fines to points deductions and even expulsion from Euro 2012.
UEFA is also studying reports that a banana was thrown toward the field from a section housing Croatia fans.
Balotelli has now been the target of reported abuse at both Italy matches at Euro 2012.
UEFA is investigating claims by a Spanish fans' group that some Spain followers made monkey chants at him during a Group C match last Sunday in Gdansk.
In a separate investigation, UEFA is seeking evidence to support claims that Russian fans made monkey noises at Czech Republic defender Theodor Gebre Selassie in Wroclaw.
UEFA pledged zero tolerance of racism in Poland and Ukraine during the three-week tournament.