The RFEF took the decision following a meeting with representatives of both clubs today, with the kick-off confirmed for 2130 local time.
The last Copa del Rey final to be staged at Real's Bernabeu home was in 2007 when Sevilla beat Getafe. Since then, Atletico's Vicente Calderon stadium has held two finals, in 2008 and again last year when Barcelona defeated Athletic Bilbao.
Real and Atletico have met four times in finals, with the Rojiblancos winning on three occasions. However, Atletico have not beaten their city rivals in any competition in over a decade.
Emilio Butragueno, representing Real at the meeting with Atletico's Clemente Villaverde and RFEF secretary general Jorge Perez, welcomed the decision to hold the match at the iconic 85,000-seater venue.
"We have agreed on everything," Butragueno said in quotes reported by Marca.
"We've shown that we have an extraordinary relationship between the two clubs.
"We had maintained in recent days to reach this agreement and we are very pleased.
"The decisive factor was the capacity of our stadium. Hopefully this is a celebration of football."
A total of 30,000 tickets will be distributed to each team.