The banana landed near Milan's Guinean defender Kevin Constant who picked it up, showed it to the referee and handed it to team mate Nigel de Jong, who threw it off the field.
Milan players sarcastically applauded the section of the Atalanta fans where the banana was thrown from.
"The incident doesn’t deserve any comments, it ruined a great afternoon,” said Atalanta coach Stefano Colantuono.
Italy's disciplinary tribunal, which meets on the day following every round of matches, will announce any sanctions on Monday.
Last season, AC Milan walked off the pitch during a friendly match away to a lower league side in protest at racist chanting by the home fans.
Villarreal were fined 12,000 euros (9,800 pounds) by the Spanish football federation on Wednesday after a fan threw a banana at Barcelona's Dani Alves during last month's La Liga match at El Madrigal. The supporter was banned for life by the club.
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