European football's governing body said Celtic had been charged for displays of an "illicit banner," adding: "This case will be dealt with by the UEFA Control, Ethics and Disciplinary Body on 22 September."
The UEFA rule in question forbids the use of "gestures, words, objects or any other means to transmit any message that is not fit for a sports event, particularly messages that are of a political, ideological, religious, offensive or provocative nature".
Dozens of Palestine flags were displayed during Celtic's 5-2 first-leg win, many of them in the new safe standing section at Parkhead.
The mass action in support of Palestine was organised on Facebook a week prior to the match hosted by Celtic on its Glasgow home ground by a group calling itself "Celtic fans for Palestine."
Celtic will probably face a UEFA fine for its fans' breach of regulations concerning political statements during games, but the club's fans have proven time and again that they believe some things are more important than money.
In 2014, UEFA fined the club after fans waved Palestinian flags during a match against Iceland's KR Reykjavik.
The club was fined about £16,000 [$20,900, 18,500 euros] over the incident.
The Scottish champions have been punished eight times in five seasons by the European governing body for supporter misconduct.
Agencies contributed to this report.