City slipped to a first defeat at Sincil Bank under Chris Sutton, but turned in arguably their best home performance of his reign.
Delroy Facey had a wonderful opportunity to open the scoring early on, but the striker missed his chance.
Chris Fagan also had two excellent free kicks saved by Martin as the Imps piled on the pressure.
Chris Herd and Fagan again both hit the post for City before Marc Richards put The Valiants into a surprise 1-0 lead.
The Imps drew level when an Eric Lichaj throw was fumbled into his own net by Vale keeper Martin. This prompted a barrage of well mannered abuse towards the keeper.
Delroy Facey then fluffed a fantastic opportunity to put the Imps level after a storming run from Nathan Baker, but the on loan strikers shot was tame and straight at the keeper.
A break from Port Vale soon brought the winner, Marc Richards taking advantage of a stray Chris Herd pass to set up ex Imp Louis Dodds, who got the customary 'I used to play for Lincoln so now I'll score' goal.
Delroy Facey compounded his horrible debut with another glaring miss at the back post after a wonderful cross. Facey could only nod his effort wide despite it looking harder to score.