Manuel Fernandes has left Benfica for Valencia despite assuring Everton boss David Moyes on Thursday that he would move to Goodison Park in "24 hours".
Fernandes spent part of last season on loan at Everton
Fernandes, who was on loan at Everton last season, arrived in England on Thursday to sort out his transfer.
He was a guest of Everton for their home game with Blackburn on Saturday after passing a medical at the club.
But the midfielder on Monday signed a six-year deal at Spanish side Valencia for a total fee of £12m.
At a news conference to announce his arrival at Valencia, Fernandes said he did not know why his transfer to Everton had fallen through.
His move to Goodison Park had been complicated because he is part-owned by a third party, the Global Sports Agency.
He had already successfully completed a medical at Goodison Park, and the contracts - which included issues of third-party ownership - were being studied by Premier League officials.
After Benfica confirmed Fernandes would join Valencia, Everton issued a statement on their official website to "clarify the situation".
"We worked hard all last week on what was a very difficult and complex three-party agreement," it read.
"Everton staff worked through the night on Thursday, finally reaching agreement with the English footballing authorities on Friday afternoon.
"A similar night's work on Friday left us satisfied that we had both addressed and agreed all issues with the other involved parties.
"However, on Saturday we were informed that another club had come in with a rival bid and despite sustained efforts over the remainder of the weekend the player joined Valencia."
Under Premier League rules, England's top clubs are not allowed to field a player owned by a third party who would have the "ability materially to influence its policies or the performance of its teams".
Everton, it is believed, were initially only planning to buy 50% of the player from Benfica for £6m, with third-party companies owning the rest, though as part of the deal the Premier League club would retain an option to buy out the rest of the player after a fixed period.
That caused problems for the Premier League, which is clamping down on all third-party transfers in the wake of the Carlos Tevez affair, and Everton then moved to buy out the other 50% from the owners.
Valencia are thought to have paid £6m to Benfica and the same amount to Global Sports Agency.
Everton have pledged to find a replacement for Fernandes before the transfer window closes on Friday.