"A disciplinary proceeding has been opened against FC Barcelona for illicit banner use and chanting," a UEFA spokesman told AFP in an e-mail.
"The case will be decided during the next control, ethics and disciplinary meeting on July 23," he added.
UEFA rules ban the use of "symbols, actions or songs that are not within the context of a sports event, especially messages of a political, ideological, religious, offensive and provocative nature."
Barcelona face a stiff fine and partial stadium closure if found to have violated UEFA rules.
During the 3-1 win over Juventus in Berlin on June 6 the club's supporters displayed red and yellow Catalan separatist flags from the stands and chanted slogans in favour of independence for the wealthy northeastern region of Spain.
Barcelona will appeal UEFA's decision, citing respect for freedom of expression of its supporters, a club spokesman said.
The club has historically had close ties with Catalan nationalism.
Barca backed a symbolic independence referendum organised in November by the regional government of Catalonia which was fiercely opposed by the central government in Madrid.
During Barcelona's 3-1 King Cup final win over Athletic Bilbao on May 30 supporters from both teams jeered while Spain's national anthem was played.
After the match Spanish Prime Minister Mariano Rajoy's office issued a statement condemning "attacks against symbols that represent all Spaniards".
Athletic Bilbao is based in Spain's northern Basque County which like Catalonia has an active independence movement.