The match, likely to be played at Kingsmeadow on Saturday November 12, is the first meeting between the two sides.
AFC Wimbledon are in their first season in the Football League, after a rapid rise through the non-league pyramid.
The were formed by Wimbledon fans after their club was moved to Milton Keynes and rebranded as MK Dons.
The Iron last met the previous incarnation of Wimnledon in 1994, when the London side were 3-0 winners in the FA Cup third round at Selhurst Park thanks to a hat-trick from Dean Holdsworth.
The away allocation will include standing and seating tickets, and will go on sale to season ticket holders from Thursday.