MK Dons set up a play-off semi-final with Scunthorpe after victory over relegated Hereford saw them finish third in League One.
Luke Howell snapped up the only goal two minutes from time when he volleyed over the top of Peter Gulacsi.
Hereford's Jennison Myrie-Williams' powerful 15-yard drive was well-saved by Willy Gueret early on.
And striker Steve Guinan had a gilt-edged chance to break the deadlock but he shot over before Howell struck.
Hereford:
Gulacsi, Gwynne, Gowling, Rose, Taylor, Myrie-Williams, Smith (Jones 87), Diagouraga, Done (Brandy 82), Guinan, Pugh.
Subs Not Used: Macleod, Veiga, Beckwith.
Booked: Gowling.
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Milton Keynes Dons:
Gueret, Cummings, Llera, Stirling, Lewington, Chadwick (Regan 77), Leven (Navarro 70), Howell, Wright (Johnson 52), Flo, Baldock.
Subs Not Used: Abbey, Wilbraham.
Goals: Howell 85.
Att: 3,224
Ref: Tony Bates (Staffordshire).
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