The 23-year-old former Manchester United centre-half, who can also play at right-back, becomes the third player in the last 24 hours to sign on at New York Stadium, following in the footsteps of fellow former Old Trafford trainees Reece James and Tom Lawrence.
Wootton has fallen out of favour at Elland Road this season and has only made four appearances, none of which came after August. He will battle it out to break up the established centre-back pairing of Craig Morgan and Kari Arnason when Rotherham play Blackpool on Saturday.