The Imps switched formation to add an extra striker and pulled a goal back from two-down but they were unable to shake an improving home side.
Mark Jones shot Wrexham into the lead midway through the first half with a lucky deflection off Lee Beevers that wrong-footed Alan Marriott and sent him the wrong way.
Chris Llewellyn added the second on the stroke of half-time, jabbing over the line when Steven Evans' downward header from Darren Ferguson's corner was going wide.
Marriott was busy all through the game and made a number of brilliant saves. He turned an early header from Danny Williams over the bar and then saved a header from Kevin Smith.
Again, when Smith cut in from the left, Marriott made the vital save and he also kept out a fierce angled drive from Josh Johnson.
Lincoln had a bright early spell but could not break through a solid home defence.
Mark Stallard was about to shoot when Evans nipped the ball off his toe and the Imps striker was out of luck again when Matt Birley's shot-cum-cross skidded passed him on the edge of the box.
Marriott made further saves from Jones and twice from Llewellyn and Johnson.
With the game slipping away, Lincoln switched to go with three strikers and it paid off with a goal when Stallard broke down the left and unleashed a 15-yard shot that gave Michael Ingham no chance.