York defender Mark Greaves scored an own goal to hand all three points to his former club Burton Albion.
Nigel Clough's side fell behind eight minutes after half time when Adam Smith collected Onome Sodje's cross and rifled the ball home from 12 yards.
Shaun Harrad equalised when he followed up after Michael Ingham had spilled Ryan Austin's 20-yard free-kick.
Burton defender Aaron Webster's overhead kick flew over the bar before Greaves's own goal.
Burton Albion:
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Booked: Pearson.
Goals: Harrad 62, Greaves 70 og.
Booked: Brodie, Rusk.
Goals: Smith 53.
Att: 3,578.
Ref: Gary Sutton (Lincolnshire).
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