County were dealt a blow when Matt McNeil was passed unfit after damaging a knee ligament at Bradford.
Michael Raynes deputised alongside Gaz Owen who again took the captain's armband.
Keith Briggs, Michael Bowler and Tommy Rowe, who all started at Valley Parade were left out with Greg Tansey, Adam Griffin and Paul Turnbull recalled.
Lincoln included former County loanee Ben Smith in goal.
County played with the wind in their sails in the opening exchanges, Liam Dickinson going closest with a far post header.
Dickinson was again involved moments later when County thought they were ahead when the popular forward smashed the ball home under the grasp of Smith, but the referee ruled it out for a foul on Hone.
At the other end Lincoln went close when N'Guessan hit a powerful shot from 18 yards that Logan pushed away for a corner.
It was County that were on top though, and mix up between Dickinson and Elding on the edge of the area had County fans with their heads in hands as The Hatters struggled to find a way through.
David Poole had an agonising miss on the half hour mark when in front of goal he put his shot wide from a wonderful Dickinson cross.
It was obvious that Lincoln struggled to deal with set-pieces, and so County continued to put crosses into the box to try and hurt them. Indeed Dickinson and Elding both went close, but things were not falling for them.
In truth Smith never had a real save to make and as efforts started to fall for Lincoln, in particular Frecklington's curling effort, County knew they had to find a way through and soon.
Smith's first save came on the 36th minute when Elding crossed for Dickinson and the big strikers looping header was saved by the former County man.
Lincoln went agonisingly close when Hone headed just wide of the far post as the first half entered the closing exchanges.
Liam Dickinson had a strike on goal saved by Smith two minutes before the break as both sides struggled to find that opening goal.
Second Half
Lincoln were ahead just minutes into the second half when Ben Wright volleyed home from after Conrad Logan failed to gather a N'Guessan cross.
The visitors were unbelievably two goals up when Ben Wright volleyed home again from a Warlow cross.
After this Gannon made a triple substitution, Proudlock replaced Elding, Rowe replaced Rose and Griffin dropped back whilst Briggs replaced Greg Tansey in the middle.
Dickinson went close with a shot from the edge of the area as County tried to salvage something from the game. It wasn't to be and in the end the score remained the same.
County went agonisingly close moments later when Proudlock's shot from a Turnbull cross went just wide of the post.
There was a moment of controversy when Adam Proudlock was sent off with a perfectly timed challenge that was plain to see. It almost ended any chance County had of getting something from the game.
Gaz Owen went agonisingly close with an effort from inside the area, this was soon followed by a Tommy Rowe strike that went just wide. It was just never going to be County's night.
County got the goal they so craved when Dickinson smashed the ball home after Smith beat out Poole's shot.
The deficit was put back to two, however, when John-Lewis made the most of some hap-hazard defending with a strike from inside the area.
A glaring miss from Dickinson moments before the end spelt out County's night.
County: Logan; Taylor, Raynes, Owen, Rose; Poole, Turnbull, Tansey, Griffin; Elding, Dickinson.
Subs: Briggs, Tunnicliffe, Rowe, Nowland, Proudlock.
