The Glasgow club have also been cited for a "kit infringement" and "blocked stairways" during Wednesday's 4-0 victory at Celtic Park.
Celtic have condemned the conduct of "a small minority of the crowd".
The club have opened their own inquiry into the banner and say they will take "appropriate action".
In the past six years, the Scottish champions have been punished on 10 separate occasions relating to misconduct from supporters during European ties.
Uefa rules prohibit the use of "any message that is not fit for a sports event, particularly messages that are of a political, ideological, religious, offensive or provocative nature".
A statement from Celtic said: "Any support for a paramilitary or proscribed terrorist organisation has no place at Celtic Park.
"The club has been consistent in condemning such conduct on the very few occasions in the past when it has occurred at Celtic Park. It is unfortunate that such a small minority of the crowd at Celtic Park last night behaved in such a way.
"We know that the Celtic support will join us in condemning such behaviour."
The kit infringement is believed to be for the wearing of training bibs with a visible sponsor name.
The case will be dealt with by the Uefa control, ethics and disciplinary body on 28 July.
Meanwhile, Celtic have been punished for disciplinary breaches in the first leg.
Striker Leigh Griffiths must serve a one-match ban for "provoking spectators" after tying a scarf to the goalposts, while there was a fine for "improper conduct of the team" after they picked up five bookings in the 2-0 win.
Celtic have been charged by Uefa over an "illicit banner" displayed during their Champions League qualifier against Linfield.