The repayment includes about €24m (£21m) in income tax and almost €25m (£22m) in fines for what authorities had described as a “very serious” infringement.
The tax agency said it would appeal to the Supreme Court and that no payment would be made until the final ruling.
The 49-year-old star lived with former Barcelona and Spain footballer Gerard Pique for more than a decade after reportedly meeting in 2010 while filming the music video for Waka Waka (This Time for Africa), the official song of the World Cup in South Africa.
The High Court said the fines were unlawful because they relied on the assumption that Spain was her tax residence for the 2011 fiscal year, “a fact which has not been proven”.
The court said the singer spent 163 days in Spain in that financial year – 20 days short of the threshold for her to be classed as a resident for tax purposes.
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