Uefa announced the decision on its website (www.uefa.com) on Thursday following a meeting of its Control, Ethics and Disciplinary Body, saying Barca had breached article 16 (2) (e) of the regulations.
The article 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".
Barca, who beat Juventus 3-1 to win their fifth European crown, has long been an outlet for fans who support Catalan independence from Spain to express their beliefs.
Supporters of the club were criticised by politicians from Spain's ruling People's Party (PP) after they whistled the national anthem at the King's Cup final at the end of May.
($1 = 0.9089 euros)