The third-tier team announced on Monday they would boycott the game unless club president Angel Lavin and the board resigned and they formed a line on the centre circle immediately after the match at the Sardinero began.
Sociedad played the ball around in their own half for about a minute before the referee consulted home captain Mario Fernandez and brought the tie to a halt.
In bizarre scenes, which brought the financial difficulties hindering many Spanish clubs sharply into focus, rival players and coaching staff embraced on the pitch as the Santander fans chanted their support for the team.
Santander lost last week's first leg 3-1 at the Anoeta stadium in San Sebastian.
Pending official confirmation, Sociedad will go through to play record Cup winners Barcelona in the semi-finals.
"Right now we have mixed feelings of sadness and a kind of joy but it is a shame it had to come to this," Santander midfielder Javi Soria said.
"We have had things clear in our minds since Monday and we have showed tonight we are a team. We hope things get sorted out because we just want to get back to playing and try to make Racing the best it can be.
"We hope there are no legal consequences because we have done this for the good of football, for the good of a city and for the whole of Spain because there are lots of similar cases and we wanted to set an example," said Soria.
Lavin was at the stadium on Thursday but did not appear in the VIP tribune, local media reported.
He showed no sign of bowing to the team's demands after their ultimatum and said in the run-up to the match he was seeking a consensus so that it could go ahead.
Sociedad are set to visit Barca in their semi-final first leg on Wednesday with the return in San Sebastian a week later.
On the other side of the draw, holders Atletico Madrid travel to Real Madrid on Wednesday in a repeat of last year's final. The return is at the Calderon the following Tuesday.
Santander have fallen on hard times since the north coast club were taken over in January 2011 by Indian businessman Ahsan Ali Syed.
Ali Syed promised to invest in the squad and said the club could become a "third force" in Spain to challenge Real Madrid and Barca.
However, they were relegated from La Liga at the end of the 2011-12 season after finishing 10 points adrift at the bottom.
Ali Syed disappeared from view and the club's crisis deepened as they dropped into the third tier (Segunda B) at the end of last term.
The future looked bleak after a capital increase in October designed to save them from ruin flopped and had to be abandoned. They remain in bankruptcy proceedings.
More may be known about their fate after a meeting of shareholders on Friday.
- Sports & Recreation
- Mario Fernandez