The young centre-back, who made two appearances in the Champions League last season against CFR Cluj, has agreed a three-year contract with the Elland Road outfit
The 21-year-old signed for the Premier League champions in 2007, making seven senior appearances for the Red Devils, including two outings in the Champions League.
Having struggled to cement a place in United's first-team squad, however, he was given several loan spells with Tranmere Rovers, Peterborough United and Nottingham Forest.
Wootton now becomes Leeds' fourth signing of the summer, after Matt Smith, Luke Murphy and Noel Hunt, and manager Brian McDermott is thrilled to have secured the youngster's signature.
"I’m delighted to have agreed the signing of Scott Wootton on a three-year deal," said the former Reading boss.
"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."