The Dons achieved one of the biggest upsets in League Cup history when they beat Louis van Gaal's side 4-0 at Stadium MK on Tuesday.
And now they have another home tie against 2013 finalists Bradford, who beat Yorkshire rivals Leeds 2-1 in the second round.
Arsenal will host Southampton in one of five all Premier League ties along with West Brom v Hull, Crystal Palace v Newcastle, Swansea v Everton and Sunderland v Stoke.
Holders Manchester City welcome Championship side Sheffield Wednesday to the Etihad.
League Two Burton, who caused a huge upset by winning 1-0 at QPR in round two, will host Brighton in the third round, while Leyton Orient - 1-0 winners at Aston Villa in the previous round - will take on Sheffield United at Brisbane Road.
In other selected ties, Liverpool face Middlesbrough at Anfield, Tottenham take on Nottingham Forest and Chelsea host Bolton.
Capital One Cup third-round draw:
Chelsea v Bolton
Arsenal v Southampton
West Brom v Hull
Crystal Palace v Newcastle
Leyton Orient v Sheffield United
Cardiff v Bournemouth
Sunderland v Stoke
Derby v Reading
Liverpool v Middlesbrough
MK Dons v Bradford
Manchester City v Sheffield Wednesday
Burton v Brighton
Swansea v Everton
Shrewsbury v Norwich
Fulham v Doncaster
Tottenham v Nottingham Forest
Ties will be played on September 23 and 24.