Kerr scored his first goals of the season, one in either half, although his goalkeeper Robert Burch was also a hero with a number of crucial saves in the first half.
The Imps went ahead as early as the fourth minute when midfielder Kerr picked up a throw-in to cut in from the left to shoot across Kenny Arthur from inside the box.
Burch then saved from Craig Lindfield, John Miles, Lindfield again and James Ryan as Accy showed the kind of form that has dragged them away to safety in the last month or so.
Lincoln could have easily played close to an hour with only ten men, but defender Lee Beevers was lucky to escape any action after a dreadful tackle on Robert Grant.
Kerr then made the game safe just five minutes into the second half when he fired home into the bottom right corner from inside the area.
This was a major blow to Stanley, who had Robbie Williams and Ryan to blame after the latter was forced off the ball by Kerr after receiving a needless ball from defender Williams.
Michael O'Connor and Adrian Patulea could have made it three for the Imps on two separate occasions, while Stanley, a shadow of the team who pressurised so well in the first half, could have snatched a consolation had Ryan's late effort not been hacked off the line.
Lincoln are now six points off the play-offs with six games still to play.