United threatened early on with Mark Hudson finding Michael Cummins with a pass but the midfielder's shot was blocked by a defender.
Cummins then caused problems for Lincoln with a deep cross into the box, but Lincoln keeper Rob Burch collected ahead of two Rotherham strikers.
United's Jamie Clarke went close to breaking the deadlock in the 24th minute when he cut in from the left and fired in a shot which brought a diving save from Burch.
From the resulting corner Clarke had an effort blocked by Scott Kerr. Rotherham kept up the pressure and Reuben Reid sent in a powerful header which flew narrowly wide.
On the half-hour Lincoln's Paul Green laid out Hudson with a bad late challenge and was lucky to escape with a yellow card.
The foul led to a melee and when referee Graham Salisbury finally restored order he also booked Lincoln's Geoff Horsfield and Rotherham's Nick Fenton.
Rotherham stayed on top in the second half and it was no surprise when they grabbed the winner in the 65th minute.
Clarke was the architect, leaving Paul Green for dead inside the box, before firing in a shot which was deflected into the path of Drewe Broughton. The big striker's header was pushed out by Burch, but Cummins followed up to fire home.
Rotherham could have scored more with substitute Ryan Taylor causing plenty of problems down the right.
Taylor broke away ten minutes from time but saw his shot saved by Burch. Then Hudson set up Taylor, but this time the sub shot over the bar.
Jamie Green got clear of the Lincoln defence in stoppage time but blasted his shot against the crossbar.
Lincoln then finally woke up and almost snatched an equaliser when Janos Kovacs beat Andy Warrington with his header, only to be denied by the woodwork.