The visitors were missing five men through injury and suspension and were forced to defend for long spells. But they held out and in the end went home with a point.
Chester were unlucky after only three minutes when a neat pass from Glenn Rule sent Ryan Lowe into the box. The striker appeared to be tripped by Lincoln centre-back Janos Kovacs but referee Nigel Miller rejected pleas for a penalty.
Lincoln's Geoff Horsfield had a half-chance when Lee Beevers fired the ball into the box but the former Sheffield United striker sent his header wide.
Lincoln went close in the 11th minute when skipper Scott Kerr fired in a free-kick from 20 yards, but was denied by a one-handed save from Chester keeper John Danby.
Chester almost cracked four minutes later when Danby was beaten by a cross from Anthony Elding. The ball fell to Horsfield whose chip was heading for the net until Paul Linwood cleared off the line.
Chester went in front with a goal out of the blue after 31 minutes. Tony Dinning touched a short free-kick to Anthony Barry who ran at the Lincoln defence before firing home an unstoppable shot from 30 yards.
When Lincoln tried to hit back they were frustrated by the Chester defence with Linwood and Dinning outstanding.
But Lincoln eventually levelled in the 48th minute when a corner from Aaron Brown was headed in by Lee Frecklington.
Lincoln went searching for the winner but could not find their way through the massed Chester defence.
Dany N'Guessan was denied by an excellent save by Danby on the hour, and then a corner from Brown caused chaos in the Chester box, but Horsfield was crowded out when he tried to force the ball home.
A 74th-minute cross from Kerr brought a rare mistake from Danby who only pushed the ball out as far as N'Guessan but the Frenchman shot widely over.
Eleven minutes from time Horsfield had a great chance to net the winner but his shot was blocked by Danby.