Late goals from Kevin Sanasy and Danny Cadamarteri could not prevent Bradford from relegation to Division Two.
Bradford had to win but Gary Smith played in Malvin Kamara for an early goal before converting Wayne Smith's cross to extend the Dons lead.
Bradford goalkeeper Mark Paston let Ben Harding's free-kick slip through his fingers for the Dons third before Sanasy converted Cadamarteri's cross.
Cadamarteri reduced the deficit with a 25-yard drive but it was not enough.
Bryan Robson's side went into the game knowing nothing short of a win would
give them a fighting chance of staying in the Nationwide First Division.
Bradford conceded their first goal after five minutes but might have equalised had Jason Gavin's header after 15 minutes not drifted wide.
The Dons should have added a second when a brilliant volley
from Nico Herzig was blocked on the line by Gareth Edds.
But Smith did eventually make it two and Gray almost made it 3-0 to the visitors before the interval but Paston was somehow able to tip his header around the post.
Shortly after the interval Paston made his blunder from Harding's free-kick - forcing
Robson to take desperate action.
The manager threw on Sanasy in place of Dean Windass - and shortly afterwards the young striker scored.
Bradford pushed forward and three minutes later Cadamarteri made it 3-2.
Cadamarteri then almost grabbed an unlikely equaliser but his drilled shot was
acrobatically stopped by Scott Bevan to leave Bradford facing life in Division
Two next season.
Bradford: Paston, Edds, Wetherall, Gavin, Heckingbottom,
Summerbee, Atherton, Wolleaston, Branch, Windass, Cadamarteri.
Subs: Combe, Bower, Forrest, Sanasy, Penford.
Wimbledon: Bevan, Hawkins, Ntimban-Zeh, Herzig, Lewington,
Kamara, Smith, Harding, Darlington, Small, Gray. Subs: McKoy,
Holdsworth, Martin, Mackie, Oyedele.
Referee: M Ryan (Lancashire).