The Gunners were thrashed 5-1 by the Bundesliga giants, who ran riot during the second half once defender Laurent Koscielny had been shown a red card for bringing down Robert Lewandowski in the penalty area to complete a 10-2 aggregate victory.
Before the match, travelling Bayern fans held up a banner which read: "without fans football is not worth a penny" to highlight the cost of ticket prices and then once the action started toilet roll was thrown onto the pitch, which caused a delay as the debris was removed.
During the closing stages, there was also a brief disruption when a supporter ran on to the field and was eventually taken off by stewards after stumbling to the floor.
A statement from UEFA said: " Disciplinary proceedings have been opened following the UEFA Champions League round of 16 match between Arsenal FC and FC Bayern MÃƒÂ¼nchen (1-5), played on 7 March in England
"Charges against Arsenal FC: Field invasions by supporters - Art
16 (2) of the UEFA Disciplinary Regulations (DR)
"Charges against FC Bayern Munchen: Throwing of objects - Art
16 (2) of DR
"No other disciplinary cases have been opened after this match."
Both clubs could be hit with fines as a result.
Source : PA