Manchester United defender Wootton, 21, joins until the end of the season having enjoyed a previous loan spell at London Road.
"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."