Manchester United defender Wootton, 21, joins until the end of the season having enjoyed a previous loan spell at London Road.
He was kept out of the side by Ryan Bennett and Gabriel Zakuani last time round but Zakuani's involvement in the African Cup of Nations is likely to give him his chance.
"Scott was very unfortunate last time he was here because Ryan Bennett and Gabriel Zakuani struck up such a good partnership, but this time, I am looking for him to be a regular starter," Posh boss Darren Ferguson told the club's official website.
"He has played in a three-man defensive line before and he is very comfortable in any of those positions. I am really pleased to get him, he has been a big part of the squad at United and they think very highly of him.
"We have got him until the end of the season. It is an area I wanted another body in because obviously Gabriel is away with the African Cup of Nations."