The Italian team have been charged with violating several UEFA disciplinary and safety regulations including racist behaviour, setting off fireworks, throwing of objects and blocking stairways.
"The cases will be dealt with by the UEFA Control, Ethics and Disciplinary Body on 22 March," the governing body of European football said.
German side Dortmund have also been charged with their fans setting off fireworks and throwing objects.
Atalanta were previously handed a suspended one-game stand closure after Napoli defender Kalidou Koulibaly was subjected to racist chants during a league game between the two sides.
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(Reporting by Aditi Prakash in Bengaluru; editing by Sudipto Ganguly)
