The Shrimps had produced a much better second-half display after trailing 2-0 at half-time thanks to goals from Morgan Whittaker and Cohen Bamall.
However, they could only pull one back after the break through Toumani Diagouraga.
Lincoln started the better and scored the opening goal of the game after just 10 minutes.
Anthony Scully found himself in space inside the box and drilled in an effort that beat Trevor Carson.
Although the effort was cleared off the line by Anthony O’Connor, the ball rebounded perfectly for Whittaker to score from six yards out.
Ten minutes later, Lincoln doubled their advantage with another swift counter.
Scully was again the inspiration with a good run into the box and a lay-off for the unmarked Bramall, who slotted the ball neatly underneath Carson.
After a poor start, Morecambe looked to find their way back into the game with Jonah Ayunga firing a low effort wide and Greg Leigh heading straight at Josh Griffiths.
Stephen Robinson’s side produced their best moment of the first half in injury time when Adam Phillips’ corner was headed narrowly over by O’Connor.
Robinson brought on Alfie McCalmont for Dylan Connolly at the break and Morecambe looked far better in the second half.
They fired themselves back into the game with Diagouraga’s brilliant finish from the edge of the box.
The Shrimps enjoyed the better of the possession and continued to threaten.
Ayunga fired wide on two occasions before wasting a glorious chance to equalise when he shot straight at Griffiths when unmarked, just six yards out.
It proved to be a vital miss as, despite their territorial advantage, the Shrimps struggled to break down a desperate Lincoln defence.
Their best chance fell to Jon Obika, who headed a cross wide from six yards out.
Lincoln went close to adding to their advantage when substitute Ben House was denied by an excellent one-handed save from Carson.
Although Morecambe continued to push, they failed to find an opening and Lincoln took three big points.
Lincoln City: Griffiths, Poole, Sanders, Eyoma (Norton-Cuffy 83), Brammall, Whittaker (House 74), McGrandles, Walsh, Maguire, Scully (Cullen 87), Marquis. Subs not used: Wright, Fiorini, Sorensen, Robson.
Morecambe: Carson, Cooney, O’Connor, Bedeau, Leigh, Phillips, Diagouraga, McLoughlin, Ayunga (Obika 67), Stockton, Connolly (McCalmont 46). Subs not used: Smith, Gnahoua, Fane, Duffus, Bennett.
Referee: Anthony Backhouse.
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