Michael Cummins scored a 65th-minute winner as Rotherham ended Lincoln's seven-match unbeaten run.
It was no more than the visitors deserved after dominating the game, striker Jamie Clarke threatening the Imps defence throughout.
Clarke forced Rob Burch into a good save in the first half and it was his effort which was blocked, leaving Cummins with an easy tap-in.
Ryan Taylor wasted two chances to make it 2-0 while Jamie Green hit the bar.
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Booked: Green, Horsfield, Kovacs.
Booked: Fenton.
Goals: Cummins 65.
Att: 4,336
Ref: Graham Salisbury (Lancashire).
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