Stockport survived a strong first-half performance from Lincoln City to secure their third successive home win.
Jake Jones went close for the Imps before Colin Larkin missed a penalty after Richard O'Donnell fouled Jones.
But the hosts improved after the break and Mark Cullen hit the post and Danny Hattersley then opened the scoring with a near-post finish.
Sean Newton got the second soon after as he curled a free-kick into the bottom corner from the edge of the box.
VIEW FROM THE DRESSING ROOM
Lincoln City boss David Holdsworth told BBC Radio Lincolnshire:
"I was disappointed to lose but I felt we played some good stuff and I can't be too critical of the players for their effort.
"A slight lack of concentration for their first goal is all I can be judgmental about but we had a number of good opportunities in front of goal and not taken those chances.
"I'm not going to blame Colin Larkin because he's played well for us. He's down in the dumps because he wanted to score and it was a big moment but that's football."