The five-times World Player of the Year is unlikely to go to prison, however.
Messi and his father Jorge were found guilty by a Catalan court last July on three counts of tax fraud between 2007 and 2009 to the tune of 4.1 million euros on image rights and were also fined 2 million euros (£1.7 million).
The court reduced Jorge Messi's sentence from 21 months to 15, however, for returning the defrauded amount to Spain's tax authority.
Neither Messi nor his father are expected to serve time in jail, as under Spanish law sentences under two years can be served under probation.
A court statement said Messi "unequivocally understood his obligation to pay tax on income obtained from exploiting his image rights...therefore it is not logical that he should ignore his duty to pay tax on them".
The Supreme Court's ruling brings an end to a case which began in 2013.
Messi, 29, and his father defrauded the Spanish tax office of 4.1 million euros between 2007 and 2009 by using a web of shell companies based in Belize, Switzerland and Uruguay to evade taxes on income from the player's image rights.
Messi, who has won eight La Liga titles, four King's Cups and four Champions League crowns with Barcelona, finished top scorer in Spain this season with 37 league goals.
He is set to play in the King's Cup final next Saturday in Madrid, the last game of the domestic season.
Messi is Barcelona's all-time top scorer and their highest paid player. He is expected to sign a new contract with the Catalan club later this summer, with his current deal expiring in June 2018.
Messi's lawyer was not available for comment.
Barcelona, who last year released a statement in support of Messi following his guilty sentence and launched a campaign in support of him on social media, have not yet commented on the Supreme Court's decision.
(Reporting By Raquel Castillo and Richard Martin; Editing by Julien Toyer and Angus MacSwan)
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