A judge in Madrid revoked a local council ruling banning the Estelada from the Copa del Rey final after Barcelona made an official complaint and appealed the decision.
The club had slammed the ruling, branding it ‘an attack on the freedom of expression’.
A statement from the club, issued after the ban had been overturned, praised the decision.
It read: “FC Barcelona has expressed its satisfaction with the judicial decision to allow the display of ‘estelada’ flags at the Copa del Rey Final against Sevilla FC this coming Sunday at the Vicente Calderón in Madrid.
“The Club thus celebrates that the judge’s decision will allow the free expression of legal symbols and banners by its members and supporters.
“The Club reiterates its commitment to the defence of the freedom of expression among its members and supporters.”
Thousands of Barcelona fans had planned to take Scottish saltires to the match to circumvent the ban.
The independence movement in Catalunya aligned itself closely with pro-independence groups in Scotland during the lead-up to the Scottish referendum on independence.
According to a report in Spain’s Mundo Deportivo newspaper, Barcelona fans had planned to wave Scottish flags as the teams took to the pitch at Atletico Madrid’s Vicente Calderón stadium, under the slogan “Nos podrán prohibir llevar una bandera, pero no nos podrán prohibir jamás la libertad” - “You may prohibit our flags but you will never prohibit our freedom”.
Government officials had claimed that banning the Estelada was part of wider security measures implemented for the showpiece tie in Madrid.
The Estelada has become a common sight at Barcelona matches at the club’s Camp Nou stadium in recent years, but the club’s association with ‘Catalanismo’ - championing and defending the rights of Catalans - has existed since at least the 1920s.
Camp Nou was closed for six months in 1925 after fans jeered the Spanish anthem. And in 1936, Francoist troops arrested and murdered club president Josep Sunyol, a prominent Catalan lawyer, journalist and politician.
Copa del Rey finals in recent years have been used by Barcelona fans to display pro-independence flags.
And Spanish King Felipe VI was loudly jeered by both Catalans and Basques before last year’s final between Barcelona and Athletic Bilbao.