County deserved the points and were always in control, but had to wait until midway through the second half to score the winner.
Lincoln struggled to create anything in front of goal and the only time they tested County keeper John Ruddy was deep into second-half stoppage time.
County should have been in front after only five minutes when James Smith set up Liam Dickinson.
The striker beat off the challenge of Daniel Hone, but his shot was kept out by the out-stretched foot of Lincoln keeper Alan Marriott.
Marriott was in action again in the 16th minute when he saved a free-kick from Michael Rose under his own bar.
Dickinson broke away five minutes later, but failed to make the most of the chance and sent his shot straight at Marriott.
County continued to create the chances and, after a mistake by Shane Clarke, Dickinson got away but took too long on the ball and Lee Beevers was able to get in the tackle.
Lincoln created their first chance in the 49th minute when Paul Green sent over a free-kick from the left. Hone escaped his marker but failed to find the target from five yards out.
But Stockport were quick to get back into the game and Dickinson wasted another chance in the 58th minute when he again beat the home offside trap.
Stockport switched to 4-4-2 in the 66th minute with Adam Proudlock coming on to join Dickinson up front.
Within two minutes they grabbed what proved to be the winner. Lincoln keeper Marriott failed to get any distance on his punched clearance and David Poole fired the ball back into the net through a crowd of players.
Lincoln went close to an equaliser two minutes into stoppage time when a shot from Jamie Forrester deflected off a defender, but Ruddy made an excellent save.