On Monday night, Everton sought to explain their part in last week's negotiations and explained how close they were to signing the player from Benfica.
A statement on the club's official website said: "Everton Football Club feels it should clarify the situation with regards to Manuel Fernandes.
"We worked hard all last week on what was a very difficult and complex three-party agreement.
"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 today joined Valencia.
"David Moyes and his coaching staff are continuing to seek the extra addition to our squad, which they feel they require for this season."