The 21-year-old’s request, which was submitted on Tuesday, was rejected by manager Roberto Martinez on Thursday morning before the club released a statement by Everton chairman Bill Kenwright.
Kenwright said in the statement on the club’s official website: “Everton Football Club has rejected a transfer request from John Stones.
“Since the start of the transfer window, we have resolutely turned down offers from another Premier League football club for our player.
“John is not for sale and he will remain a highly valued member of our first team squad.”
Toffees manager Martinez has insisted he has “great plans” for centre-back Stones.
A determined Martinez has been adamant throughout the saga of three bids from Chelsea, the last for £30million, that the defender is not for sale and he is maintaining that position.
Despite Stones asking to leave the Toffees boss is confident he can not only keep hold of a prized asset but persuade the player he has a vital role to play going forward.
“During this tough period we are going to be there for him,” he said.
“We have great ambition, desire and great plans for John. We want to be a winning team and we need to keep our best performers and clearly John is big part of our future.
“We are a big football club with an incredible tradition and we will carry on giving him everything we can.
“As a young man you are under massive pressure and you are going to get influences.
“We are going to look after John. We are going to understand him.”
Martinez has long since railed against a situation which allows the transfer window and its fevered speculation to drag on for a whole month once teams have returned to competitive action.
He has some sympathy for the players caught in the middle and directed his anger at the governing bodies who allow it to continue to the detriment of those involved.
“There is a bigger example for the football authorities. Up and down the country every dressing room has similar situations,” he added.
“Are we going to end up with players feeling bad about themselves, not to be proud of representing their colours?
“It becomes an unsustainable position. It needs to be changed. The players are human and human beings deserve the time to think about the next step of their careers – but that cannot be done when there is an official game.
“I feel let down by the football authorities in this position. We should look after our players and we will make sure we will look after John.
“Going away from John’s situation we have to understand when the window is open and there are official games we need to give some value to contracts.
“We have contracts for players when they are injured but when they are well they can be moved around.
“We need to bring a more serious touch to being a part of the football club and making sure contracts are important in order to fulfil your potential at a club and have a good future.”
While Stones had one of his worst games for some time against his former club the performance of half-time substitute Gerard Deulofeu, in particular, was one of the major positives at Oakwell.
The Catalan, also 21, needed time to adjust during his loan spell at Goodison the season before last but having signed permanently from Barcelona in the summer he showed he has already progressed as a player.
“His pace and penetration and ability in a one v one situation was probably something that inspired our second-half performance,” said Martinez.
“At the end it was quite tough for him as it was not planned for him to play any more than 45 minutes but he adapted well and he can only benefit from that. It was a really good display.”