MK's 6-1 win over the non-league side means that following AFC`s victory over York, the two will go against each other at the start of December in what will no doubt be emotion-fuelled affair.
AFC were formed in 2002 by supporters of Wimbledon FC who were unhappy with the Football Association`s decision to allow their club to relocate to Milton Keynes.
They started out in the Combined Counties League, the ninth tier of English football, attracting 2,449 people to their first ever game. In 2011 they were promoted to the Football League.
After the location change, Wimbledon FC played in Milton Keynes for two seasons before changing identity completely to Milton Keynes Dons. In 2007 the club conceded the history of Wimbledon FC, including its 1988 FA Cup Final win, could return to the London Borough of Merton.
Some bitterness does remain, though, most notably through a campaign for Milton Keynes to drop the `Dons` part of their name.
After the two sides were provisionally drawn together, the Wimbledon Independent Supporters Association released a statement which included the line: "WISA once again calls upon Milton Keynes to drop the name Dons from their name, a name that remains a prominent reminder, that they stole a Football League place through the theft and franchising of Wimbledon FC, despite acknowledging that they are a new club representing the community of Milton Keynes."
Like AFC Wimbledon, the Dons too have enjoyed success. In 2008 they completed a League Two and Football League Trophy double.
WISA has expressed a desire for the game not to be played and has promised to speak with the club and its supporters about whether or not it should be.
After their victory over York, AFC manager, Neal Ardley, a former Wimbledon FC player, said: "I'd play against anyone."