A tale of two halves at Sincil Bank saw the Blues emerge with a point, but manager Steve Burr will be entitled to feel it should have been all three.
Lincoln were the better side in the first period and took a deserved 1-0 lead into the break, although that was as much down to the visitors sluggish performance.
It was a different story in the second half and the Blues would be returning home with a win but for Imps keeper Nick Townsend, who made a string of important saves.
Having made nine changes for the midweek Cheshire Senior Cup exit to Macclesfield Town, Burr reverted to the starting side from the 2-1 win over FC Halifax Town.
On-loan keeper Aaron Chapman, so impressive in his debut against the Shaymen before injury intervened, recovered from his dislocated hand to take his place between the sticks.
Right back Michael Kay and attacking midfielder Craig Lindfield came onto the bench to replace Paul Linwood and Jamie Reed.
Imps boss Gary Simpson had seen his improving side pick up nine points from four league games during February and fielded the same team that defeated Kidderminster Harriers 2-0 last time out.
In-form striker Ben Tomlinson looked to be the biggest danger for the hosts with eight goals in his last six appearances.
Chances were rare for both teams early on, although the Blues shaded possession and managed to create a couple of promising openings.
Lincoln grew into the contest and took the lead on 16 minutes through Delano Sam-Yorke, but the opener was poor from the visitors perspective.
Tom Miller hurled the ball into the area from the right and Chapman contemplated coming but decided against and the ball fell to Sam-Yorke, who tapped home from inside four yards.
Craig Mahon had a header deflected behind two minutes later as the Blues looked to get back on level terms, but the home side then took charge.
Ex-Chester City left back Sean Newton sent over a succession of testing corners as the hosts put Chapman under pressure and then forced the towering keeper into a save with a fizzing low drive.
Missing the enthusiasm evident in the Halifax game, Chester were unable to establish a foothold in the game and looked every bit a team in trouble.
Regardless of their team's uninspiring start, the 250 or so travelling supporters provided constant encouragement and Lewis Turner forced Imps keeper Nick Townsend into a good stop with a stinging drive on 30 minutes.
Lincoln continued to create the clearer opportunities with Sam-Yorke failing to connect with Miller's drag back and Todd Jordan side-footed wide from close range with the goal begging.
Chester could not keep hold of the ball for any prolonged period of time and the final chance of a fairly forgettable 45 minutes fell to Sam-Yorke, who scuffed wide under pressure from Ross Killock.
After a below-par first half, the Blues needed to come out strong and it took only seven minutes for the ideal response to arrive.
Matty Taylor brought a long, raking pass under control, turned Thierry Audel inside out before slamming the equaliser underneath Townsend and into the bottom corner.
Having drawn level, the visitors almost went ahead two minutes later when Matty Brown sent a thumping header inches over the bar from a John Rooney free kick.
Lincoln had the perfect chance to go back in front on 62 minutes when Miller sent over another long throw and Brown handled the ball as he tried to head clear.
Referee Colin Lymer awarded the penalty without hesitation and Imps skipper Alan Power - who scored a spot kick in the 3-3 draw between the sides in December - stepped up but Chapman used all of his 6ft 8ins to save down to his right.
Townsend made an equally important save at the other end minutes later, just about keeping out a Killock header before making another stop from Gareth Seddon's speculative volley.
Burr threw on Jamie Menagh - the match winning hero against Halifax - for the last 20 minutes and he brought a decent save out of Townsend with an angled strike.
Both sides pushed forward in the closing stages as the game opened up but it was the Blues who looked the most likely.
Rooney sent a half-volley just over from 20 yards and came even closer late on as Townsend tipped his low strike onto the post with the ball rolling back into his grateful hands.
Lincoln committed men forward with the clock running down and the impressive Sam-Yorke forced Chapman into a save before the big keeper spilled Miller's long throw but Nat Brown flashed over from close range as time ran out.
Lincoln City: Townsend, Miller, Brown, Audel, Newton, Jordan, Power, Sheridan (Robinson 63), Adams, Tomlinson, Sam-Yorke.
Subs: Rowe, Preece, Gray, Nolan.
Goal: Sam-Yorke 16.
Chester FC: Chapman, Turner, Brown, Killock, Heath (Mainwaring 21), Rooney, Jarrett, Bond, Mahon (Menagh 68), Taylor, Seddon.
Subs: Kay, Danby, Lindfield.
Goal: Taylor 52.
Booked: Heath, Taylor, Brown.
Referee: Colin Lymer (Hampshire)