Barca confirmed on Wednesday that European soccer's governing body, which prohibits political demonstrations at matches, had begun proceedings but added that the club did not yet have an official reaction.
Barca beat Juventus 3-1 in the showpiece match at Berlin's Olympic stadium to clinch their fifth European Cup.
Josep Maria Bartomeu, who is standing for re-election as Barca president in this month's poll of members, defended the club's fans and said both sets of supporters had shown "exemplary" behaviour at the match.
"UEFA needs to get to know much better what Barca is and what Catalonia is," he said at a campaign rally.
"It (Barca) is a democratic club which respects freedom of expression and any demonstration by its members is legitimate," he added.
Barcelona are a source of pride for many independence-minded Catalans and fans often take the chance at matches to emphasise the region's separate identity from the rest of Spain.
The club came under fire from the ruling People's Party (PP) after May's King's Cup final against Athletic Bilbao, when the national anthem was roundly whistled by both sets of fans despite the presence of King Felipe at Barca's Nou Camp arena.
Bilbao is in the Basque Country, where many people are also in favour of independence from Spain.
(Reporting by Iain Rogers, editing by Ken Ferris)
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