European soccer governing body UEFA said in a statement that the Bundesliga champions had been charged over a "field invasion" by the fans plus the display of a banner containing a "message of an offensive nature" following the match.
UEFA said the case would be heard on May 31 but did not give further details.
Two of the fans attempted to take a photograph with Real forward Cristiano Ronaldo before being chased away by stewards. The Portuguese was unmoved by the incident as video footage showed him scratching his face and grinning.
(Writing by Brian Homewood in Bern; editing by Sudipto Ganguly)
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