Cuper managed to lead the Spanish side to just one victory in their opening 13 Primera Liga games this season.
Cuper told his squad about his exit before training on Tuesday.
Danish legend Michael Laudrup has been linked with the job as Racing Santander boss.
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Chelsea have struggled to build momentum in the opening stages of the campaign and are currently looking over their shoulders at the relegation zone.
Who of Europe’s top strikers will move to England this summer?