Racing - top of the Spanish second-tier - trailed 3-1 after the first leg, but played less than 60 seconds of the return clash at their El Sardinero home on Thursday.
The boycott was expected, with Santander captain Mario Fernandez announcing on Monday that they would refuse to take the pitch if the club's board remained in place.
Racing's players cited up to six months of unpaid wages as the reason for the decision, and they have called for president Angel Lavin to step down.
Their threat stepped up when it emerged that unless the entire board resigned before the match, the game would not go ahead.
Racing did take the pitch, but it was purely for show, with the players linking arms in the centre circle as soon as referee Jesus Gil blew his whistle to signal the start of the match.
The coaches and substitutes also linked arms on the sidelines and after Sociedad passed the ball among themselves for a short while, they kicked the ball into touch.
And when Santander refused to take the throw in, Gil decided to suspend the match - meaning Sociedad will progress to the competition's last four, where they will play Barcelona.
The Racing players were embraced by their opponents, who shook their hands and hugged them, before they were applauded and cheered by the home fans.
