The 21-year old centre-back has penned a three-year deal with the Whites after coming through the United youth academy.
Leeds boss Brian McDermott was delighted to secure the services of Wootton who has had loan spells with Tranmere Rovers, Peterborough United and Nottingham Forest and has also experienced the Champions League with United.
"I'm delighted to have agreed the signing of Scott Wootton on a three-year deal," said McDermott.
"He's a player who has played in the Champions League and someone we feel will develop with us in the coming years.
"I want to say thanks for the owners in doing the deal and bringing another young player to help us go forward."