Atleti will now host the match as a result, with Real Madrid refusing to make the Santiago Bernabeu available for their rivals due to planned construction work.
The Catalans are looking to defend the trophy they have won in each of the past two seasons, defeating Sevilla at the Calderon last year to follow up a victory over Athletic at Camp Nou in 2015.
They also defeated the Basque club on Atletico's turf at the end of the 2011-12 season.
Since hosting the Copa final for the first time in 1973 following its opening six years earlier, the Calderon has been awarded the match 13 times.
Next season Atletico will move to the Wanda Metropolitano, a new 73,000-seater stadium on the site designated for Madrid's failed bid to host the Olympic Games in 2016.
The Calderon is set to be demolished once the season has ended and replaced with a waterfront park on the banks of the Manzanares river, where it sits.