"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 band the use of "symbols, actions of 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.
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.
Athletic Bilbao is based in Spain's northern Basque County which like Catalonia has an active independence movement.
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