The defender has been on loan with the Lions since October, making 11 appearances for the London club and forming a partnership with Danny Shittu at the heart of defence.
Beevers came through the academy at Hillsborough, and has made 161 appearances for Wednesday.
He was voted the club's player of the year in 2008, but struggled for first team football under both Gary Megson and Dave Jones, moving on loan to MK Dons last season.
According to Wednesday's official website, the fee for the defender is undisclosed and Beevers will join Millwall permanently on 1 January 2013.
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