Charlie MacDonald gave Karl Robinson's side the lead on the stroke of half-time before Darren Potter doubled their advantage two minutes after the break.
Lee Miller reduced the arrears on 51 minutes, before Dons captain Dean Lewington restored the two-goal margin just after the hour mark.
With Charlton not playing until Monday, Sheffield United took advantage to go second ahead of the Addicks with a 4-0 win against Bury at Bramall Lane.
Goals either side of half-time from Chris Porter and Nathaniel Mendez-Laing put the Blades in control, before Matthew Lowton and Norwegian Erik Toone added further gloss to the scoreline on 70 and 83 minutes.
Brentford went fourth with a 1-0 win at Walsall - Clayton Donaldson with the only goal - while Hartlepool's 2-0 win ensured Exeter made the long trip back to Devon with nothing.
Huddersfield remain unbeaten after sharing a 1-1 draw with Oldham, while Tranmere were held to a goalless draw by Yeovil at Prenton Park.
At the bottom of the table, Leyton Orient claimed their first point at the sixth attempt, claiming a 0-0 draw at Chesterfield - though the two sides remain bottom and second-bottom respectively.
Chris Beardsley scored twice as Stevenage ran out 4-2 winners against Rochdale, while late goals from Krtstian Pearce and Cristian Montano gave Notts County a 3-1 win over Bournemouth at Meadow Lane.