Mackie, a former youth player at Starks Park, was one of the players revealed by The Scotsman to have been made available for a move last month alongside Melker Hallberg and Scott Allan.
Like Allan he remained in Edinburgh but has now agreed a return back to Fife to see out the remaining five months of his Hibs contract out on loan.
Mackie left Raith in 2016 and made 22 appearances at Hibs while also earning a Scotland under-21 call-up and could be in contention for a place at Parkhead on Sunday when Rovers face Celtic in the Scottish Cup last 16.
Describing their former player as “quick, athletic and with a great range of passing” Rovers view the 23-year-old as a replacement for Tom Lang, who suffered an ACL injury last weekend and faces the rest of the year on the sidelines.
Manager John McGlynn said he was "delighted to add Sean to the squad in light of the injury sustained by Tom Lang, consequently leaving us short in the defence, Sean can play in a few positions, predominantly a left back but can also play in central defence and in central midfield, his experience will be invaluable from now until the end of the season”.
McGlynn had earlier this week apologised for one of Raith's other signings, David Goodwillie, after widespread condemnation, protests and outcry over the deadline day recruitment.