The incident occurred during Celtic's 4-3 defeat in Croatia, in the final Group D encounter.
UEFA released a statement on Tuesday declaring that the Scottish Premier League leaders are being investigated, although a final decision will not be reached until the week of Celtic's last-32 meeting with Inter in February.
A UEFA release read: "Disciplinary proceedings have been opened following the UEFA Europa League group D match between GNK Dinamo Zagreb and Celtic FC (4-3), played on 11 December in Croatia.
"Celtic FC: Charges: Crowd disturbances - Article 16 (2) (h) of the UEFA Disciplinary Regulations.
"The case will be dealt with by the UEFA Control, Ethics and Disciplinary Body on 19 February 2015."
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