The third-tier team formed a line on the centre circle immediately after their cup clash against Real Sociedad started and the match was abandoned soon after.
Sociedad, who won the first leg 3-1, kept possession before kicking the ball into touch and referee Jesus Gil called an end to proceedings.
Santander players were last paid in September 2013 and warned the club's hierarchy of their plans days prior to the encounter.
Fernandez, whose team were embraced by their opponents and applauded by the fans, thanked Santander supporters.
"Obviously without the support of the people it would have been much difficult," he said.
"And I am very worried about the future of the team and about the feelings of the kids."
Santander are top of the Segunda B table on goal difference and have set their sights on promotion this season.
Fernandez said it had been a difficult week for the players, but hopes they can return to normal training ahead of Sunday's clash against Cultural Leonesa.
"At the moment, tomorrow we will train because we have to do it and we will see what will happen tomorrow," he said.
"The league is our future, getting promotion is our future, and we have to train and be in the best shape.
"Obviously, our head is not in the best conditions because it is been a week when we could not training well, because the player is thinking in another things and we need normality as soon as possible if we want to save this team."
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