Wootton, 21, will join the Championship outfit on a three-year contract.
The Liverpool-born defender featured under Sir Alex Ferguson in last season's Capital One Cup ties against Newcastle United and Chelsea, plus gained experience in the Champions League. He's previously enjoyed loan spells with Tranmere Rovers, Peterborough United (twice) and Nottingham Forest.
Wootton won plenty of Reserves silverware during his time at United, including the Lancashire Senior Cup earlier this month. The centre-back arrived from Liverpool in 2007 and has since proven his leadership qualities and pedigree on the pitch.
Leeds manager Brian McDermott said: “I’m delighted to have agreed the signing of Scott Wootton on a three-year deal. 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.”