AFC will travel to stadium:mk in early December to take on the club that replaced the original Wimbledon FC and relocated to Milton Keynes almost a decade ago.
It will be the first meeting between the sides but many AFC fans plan to boycott the match as they do not want to recognise the 'franchise' club that took their league position and still uses the name Dons.
However, Winkelman insists the tie against the club formed in the wake of that relocation, and who have battled back to the Football League with five promotions in nine years, will help both clubs put a controversial past behind them.
"It was inevitably going to happen sometime," Winkelman told Sky Sports News. "We are very keen to get this game played and get it done and dusted. There's obviously been a lot of history and water under the bridge over the last 10 years but it's a game the whole football world could be looking forward to. We certainly are. It's history in the making.
"For whatever reasons there will always be that controversy surrounding the clubs but this is a chance to get both on a football pitch and play some football. We will be able to look forward rather than back into the past.
"I hope people will see the amazing things which have come from Wimbledon FC, ie the two clubs, AFC Wimbledon and the Milton Keynes Dons."