The Iranian billionaire, 60, has been announced as the club's new major shareholder after selling his 15% share in Arsenal to Alisher Usmanov.
The deal, and its ratification, ends a decade-long search for investment by chairman Bill Kenwright.
Moshiri may attend his first game since the deal when Everton host Chelsea in the FA Cup on Saturday evening.
Moshiri's approval was a formality given his association with Arsenal but the Premier League needed to conduct checks for the Owners' and Directors' Test before confirming the deal.
Moshiri bought the 23% holding of former Everton director Robert Earl while Kenwright and board member Jon Woods diluted their shares to make up the rest of Moshiri's purchase
Kenwright, who bought Everton from Peter Johnson for £20m in 1999 and indicated his willingness to sell as far back as November 2007, has described Moshiri as "the perfect partner to take the club forward".
Farhad Moshiri's 49.9% investment in Everton has been formally approved by the Premier League.