Wimbledon's fate had long been on the cards and beaten FA Cup semi-finalists Sunderland merely confirmed the club's relegation from Division One.
Despite their tough clash against Millwall in the FA Cup on Sunday, the visitors overcame any signs of tiredness to take the lead through Marcus Stewart on the stroke of half time.
Malvin Kamara briefly offered Wimbledon hope by equalising midway through the second half but substitute Darren Byfield notched the winner with his first touch on 73 minutes.
Gillingham are also deep in the relegation mire after a 3-0 defeat at home to Wigan which lifted Paul Jewell's side into the play-off spots.
Nathan Ellington and Jason Roberts had the visitors in command before the break and Alan Mahon netted midway through the second period.
Crystal Palace survived a late rally from Rotherham to claim a 2-1 triumph at Millmoor.
Julian Gray and Neil Shipperley scored inside the opening 27 minutes but Michael Proctor's 85th minute strike was merely a consolation as Rotherham also face a fight for survival.
