The Spanish third-tier side, who are in bankruptcy proceedings, trailed 3-1 from the first leg in Sociedad, but played less than 60 seconds of the return game at El Sardinero on Thursday.
Captain Mario Fernandez had revealed on Monday that the second-tier outfit would refuse to take the field if president Angel Lavin and the club's board did not step down prior to the game, with players citing up to six months of unpaid wages as the reasoning behind their move.
Racing's players did take the pitch, but immediately linked arms in the centre circle as Sociedad passed the ball in their own half before referee Jesus Gil brought the match to a halt.
Reports in Spain have since suggested that Lavin and the rest of the board have been voted out following a shareholders' meeting, with former player Juan Antonio Sanudo said to have taken over.
Sociedad progressed to the semi-finals as a result of the abandonment and will face Barcelona in the last four.
However, Santander will not be permitted to compete in the 2014-15 tournament and have been fined €3,006 following a ruling by competition officials.
A statement from the Spanish Football Federation (RFEF) read: "In accordance with the provisions of article 77.1. a) of the Disciplinary Code of the RFEF, the club may not participate in the next edition of the Copa del S.M. Rey.
"Pursuant to paragraph three of the aforementioned article 77 of the RFEF disciplinary code, it is appropriate to impose Racing Santander with a fine to the amount of €3,006."
Despite the Spanish governing body's decision, Santander's players have received the backing of world player union FIFPro.
"The players have taken a drastic decision," FIFPro President Philippe Piat said. "But this clearly illustrates how far their desperation had gone. The players had no alternative but to opt for this measure.
"The action of the Racing players is a new signal, warning that it's essential to do something urgently in order to save football."
