The Imps needed just a point to be sure of their place, but made hard work of things. They were second-best to Chester in the early stages and should have gone behind in the 22nd minute.
Home midfielder Scott Kerr brought down Chester's young striker Chris Holroyd inside the box with a rash challenge. Referee Kevin Friend pointed straight to the spot and Holroyd picked himself up to take the kick.
The youngster, a prolific scorer in youth football, but yet to net for the first time in the Football League, made a hash of his effort, sending it almost straight at Lincoln keeper Alan Marriott, who saved easily.
Lincoln ventured forward for the first time six minutes later when Lee Beevers broke down the left. The defender sent in a dangerous cross to the far post, but Chester were saved by a timely interception from Kevin Sandwith.
Lincoln, who had scored only one goal in their previous six games, stepped up a gear after the break but it needed a mistake to give them the lead. Chester centre-back Dave Artell slipped as he tried to play the ball forward and Jamie Forrester took full advantage.
The former Leeds striker broke into the box and drew the Chester keeper John Danby before setting up Mark Stallard. The striker was left with an easy tap-in and made no mistake.
That only inspired Chester to hit back and they went on the attack looking for an equaliser.
Caretaker manager Simon Davies, in charge for the first time, introduced Simon Yeo in the 72nd minute and the striker should have levelled the score. Lee Steele did well down the right before picking out Yeo with his cross. The former Lincoln man had the time to pick his spot but completely missed the ball from six yards out.
Yeo did better five minutes from time when he forced the ball home after Marriott could only push out an effort from Jamie Hand, but the effort was ruled out for offside.
Lincoln finally got their second goal in stoppage time when Chester defender Sandwith was penalised for handling a cross as the ball flew across the box. Forrester took the penalty and fired low into the bottom corner of the net, beating the despairing dive of Danby.