"It was an inconsiderate and inadvisable gesture that hooks in with the overall problem of violence around football," said President of the Republic.
Totti was sent off for a horrific lunge on Balotelli during Roma's Coppa Italia Final defeat to Inter on Wednesday.
"There are forms of savage fanbases in football that spur on intolerable violence. Today they are seen in the stadiums, who knows where they could go tomorrow.
"It is a worrying phenomenon and the football clubs should react more strongly."