In a repeat of the opening-day League Two fixture, Lincoln were quick out of the traps with Scott Kerr firing over the bar inside the first minute.
Chances were few and far between as the game went on and Rotherham's Kevin Ellison had tthe only shot on target in the first half when his 30-yard free-kick was saved by Joe Anyon.
Debutant Jeremiah Ani headed over from Ellison's cross and then Ani headed on to set up Le Fondre just before the break but his first time effort was also too high to trouble Anyon.
But Le Fondre made amends two minutes after the break. Picked out by Tom Newey on the edge of the box, the prolific striker went for the right-hand corner, but his shot deflected off Moses Swaibu and into the other corner, giving Anyon no chance.
And there could have been a second minutes later when Ryan Cresswell's clever touch set up a shooting chance that whistled wide.
As the Millers pushed for another Le Fondre was blocked on the line and Jason Taylor's low shot was well saved by Anyon as Rotherham eased through into the next round.
Source: PA