Paratici initially stepped back from his role at Spurs on March 31 following his ban made worldwide by FIFA.
The Italian was handed a 30-month suspension from the game in January after his former club Juventus, where he worked for 11 years, were found guilty by an Italian court of false accounting.
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A day after his appeal against the Italian Football Federation (FIGC) ruling was rejected, Tottenham confirmed his departure as the ban “prevents Fabio from fulfilling his duties”.
Paratici is still awaiting the result of his appeal to FIFA against their extension of the ban worldwide. He denies any wrongdoing – as do the 11 other directors and Juventus as a club – over the financial mismanagement case.
Tottenham chairman Daniel Levy said: “This has been a stressful time for Fabio and his family. We wanted to ensure that we allowed for due process to be followed. Fabio is a man who lives and breathes football – we wish him well.
Tottenham added Paratici has taken the decision “to focus on his legal position in respect of the FIGC and FIFA rulings”.