On another foul night on a boggy DVS surface, Ronnie Moore gave home debuts to new recruits Gary Roberts and Adam Rundle in a new look midfield and the Millers started brightly.
Indeed it was Rundle cutting in from the right that created the first chance on 8 minutes, before Kevin Ellison headed another cross from the on loan winger wide inside the first quarter.
Lincoln 'keeper Rob Burch was much the busier, as he twice denied the Millers before the break.
Firstly Burch tipped over Ellison's effort from 10 yards from Le Fondre's pull back and then he denied Nick Fenton, with Le Fondre's rebounded effort going over for a corner.
On 37 minutes Le Fondre opened the scoring as he raced clear of two Imps defenders onto Tom Pope's long ball, burst into the box and crashed a shot past Burch into the roof of the net.
Scott Kerr had the best chance to level matters for the visitors just before the interval but his volley was tipped over by a flying Andy Warrington.
After the break the Imps enjoyed the majority of the ball, but had to wait until 20 minutes from the end for their only real effort at goal as ex Rotherham player Jamie Clarke set up sub Rene Howe, who shot wide.
The Millers huffed and puffed after some visiting pressure but with 10 minutes left Le Fondre sealed it with another superb goal, as his powerful bicycle kick from Pope's cross from the right thundered into the net.
The forward had the chance to crown a perfect night with a hat trick late on as Kovacs brought him down in the area, but he side footed the penalty wide as Burch went the wrong way.