City struggled to create any chances in the first 45 minutes but virtually camped in the Port Vale half after the break.
But despite intense pressure from the home team, Vale held out with keeper Joe Anyon and centre-back Luke Prosser in outstanding form.
Vale played new signing Dave Brammer in a defensive role in front of the back four and the tactic worked perfectly as Lincoln struggled to create anything before he was subbed in the second half.
Lincoln had a left-off after only 14 minutes when a slip up by Danny Hone gave Vale possession, but Marc Richards found his way blocked by Janos Kovacs.
Vale went in front with what proved to be the winner in the 25th minute. Lee Collins sent a long free-kick into the Lincoln box which was headed out by Kovacs straight to David Howland.
The midfielder had time to pick his spot from outside the box and fired straight into the net, giving City keeper Rob Burch no chance.
Lincoln appeared to be denied a penalty just before the break when Anthony Griffiths tripped Adrian Patulea.
City made a change at the break with Stefan Oakes coming off to be replaced by Aaron Brown.
Lincoln looked a different team in the second half, but despite plenty of pressure still looked vulnerable to Vale's counter-attacking play.
Lincoln should have levelled in the 73rd minute when Lee Beevers forced his way through, only to see his shot saved by Anyon.
Prosser was yellow-carded in the 82nd minute and from the resulting free-kick Brown forced another excellent save out of the keeper.
But Vale should have scored a second goal two minutes from the end. A shot from Luke Rodgers came back off the post to Richards, but with a gaping goal in front of him the striker failed to hit the target.
Lincoln managed one last attack but Kevin Gall wasted a good chance when he headed straight at Anyon from six yards.