The Imps struggled to find a way through the Chester defence and things looked bleak early in the second half when they went a goal down and lost midfielder Dean Keates, who was red carded for an off the ball incident.
Lincoln stormed back and made Chester pay for their indiscipline.
Lincoln hardly had a look in during the opening half and should have been a goal down at the break. Chester's Carl Regan produced a great cross from the left which found the head of Marcus Richardson, but the striker's efforts were superbly saved by Lincoln keeper Alan Marriott.
The second half was a different story with both teams creating plenty of chances. The turning point of the game came in 47th minute when Lincoln's Gary Birch put Derek Asamoah in the clear.
The striker blasted his shot but Chester keeper Chris MacKenzie made a point blank save. But in doing so, he suffered a broken thumb and had to be led off the field with youngster Brian Brookfield coming on to replace him for his senior debut.
In fact it was Brookfield's first touch which started the move leading to Chester taking the lead. His clearance found Richardson on the right flank and the former Lincoln man took advantage of hesitation in the home defence before firing his shot into the bottom corner.
Things looked even worse for Lincoln nine minutes later when Keates threw a punch at Ryan Lowe as the player waited for a corner to be taken. Referee Grant Hegley immediately red carded the Lincoln man.
The decision seemed to spark a Lincoln fight back and they almost scored in the 66th minute as Asamoah beat three defenders on the edge of the box, but his final shot was blocked by the legs of Brookfield.
Two minutes later, Lincoln drew level. Paul Mayo sent a free-kick into the box which was swept home by Richard Logan for the striker's first goal for the Imps since arriving on loan from Peterborough.
Within two minutes Lincoln went in front when Mayo burst into the area and was tripped by Tom Curtis. Despite Chester's protests ref Hegley awarded the spot-kick.
Brookfield went the right way but Mayo's penalty had too much power and ended up in the bottom corner.
Chester looked certain to level the game in the 72nd minute, but Ben Davies saw his shot pushed out by Marriott. The ball came back out to substitute Abdou Elkholti but his effort was blocked by the body of Gareth McAuley.
Chester boss Keith Curle was sent to the stands in the 78th minute for something he said to the referee. But Chester's misery was completed in stoppage time when Asamoah ran through and beat the keeper to a long ball before walking it into the net.