Stones, 18, has signed a five-and-a-half-year deal with Everton after passing a medical and agreeing personal terms.
An England Under-19 international, Stones - who is believed to have cost Everton around £3m - rose through the ranks at Oakwell and made his first-team debut in December 2011.
He has made 28 appearances since, scoring his first goal in the 4-3 victory over Rochdale in the Capitan One Cup.
The 6'2" defender - who also held talks with Wigan - told Sky Sports News: "I'm very happy.
"I was waiting for the call - it was Everton or Wigan. I decided Everton and I'm very pleased with it. It's a great club, with a great manager and I'm looking forward to it.
"I spoke with Wigan, they were very good to me, so thank you to them for the offer, they were very good.
"I've met David Moyes already, he's a nice man. It's such a good club, with the players here I feel I can learn for them. What a good place to be."
He added on the Barnsley website: "I would like to take this opportunity of thanking everybody at Barnsley for helping me in my development.
"They include Ronnie Branson and all the academy staff; Keith Hill and David Flitcroft for giving me the chance to play first-team football. Also all the backroom staff such as Guy Proctor, John Lucas and Craig Sedgwick.
"They are just some of the people who I owe a debt of gratitude to and I wish Barnsley every success for the future."
It was one in, one out for Everton on transfer deadline day with striker Magaye Gueye - who has appeared just six times this season - heading to French club Brest on loan for the rest of the season.