Uefa announced the decision to fine the Spanish champions on Thursday following a meeting of its Control, Ethics and Disciplinary Body, saying regulations had been breached.
But the club, which defeated Italian club Juventus 3-1, immediately said that it did not agree with the decision and would be considering an appeal.
"FC Barcelona respects Uefa's decision that was relayed to the Club on Thursday in relation to the Champions League final in Berlin," said a statement from the club.
"However, it does not agree with that decision, especially in the light of the Uefa delegate's description of the Barça members and fans' behaviour as excellent, both before, during and after the game, as stated in their report,"
The club said it could launch counter action.
"With the aim of defending the rights of the Club and its members and while respecting current legislation, the Club's legal services will consider the possibility of questioning the fine announced today, Thursday.
"Our conviction is that the rights of the Club and members are not incompatible with current legislation."
Uefa ruled that La Liga side breached article 16 of the regulations, which prohibits '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'.
The football club have long been an outlet for fans who support Catalan independence from Spain to express their beliefs.
The club also faced sanctions after fans booed and whistled to drown out the national anthem during the King's Cup final at the end of May in Camp Nou.