Nathan Peat's late winner sent York to the top of the Conference table.
Clayton Donaldson had put the home side ahead when he found the net from Craig Farrell's cross but Andy Ducros found space to level before half time.
Mark Convery restored York's lead from Donaldson's cross only for Burton to equalise for a second time when Gary Rowett headed in Keith Gilroy's corner.
But Burton had Ryan Austin sent off for a professional foul on Donaldson and Peat scored the resulting free-kick.
York: Evans, Craddock, Dudgeon, McGurk, Peat, Convery, Bishop, Panther, Bowey, Donaldson, Farrell.
Subs Not Used: Reid, Lloyd, Greenwood, Webster, Parslow.
Goals: Donaldson 8, Convery 61, Peat 90.
Burton Albion: Poole, Rowett, Tinson, Austin, Webster, Corbett (Holmes 62), Fowler, Stride, Ducros (Gilroy 71), Clare, Scoffham (Harrad 78).
Subs Not Used: Henshaw, Shaw.
Sent Off: Austin (90).
Booked: Clare, Holmes.
Goals: Ducros 50, Rowett 73.
Ref: S Cummins (Runcorn).