Lincoln never really recovered from conceding a goal after two minutes and although they had chances in the first half the Imps were two down at the break.
The first goal was a scorching low drive from the edge of the box by midfield-dynamo Jay Smith, the ball flashing just inside Alan Marriott's right-hand post.
It took Lincoln some time to get themselves into the game and when they did so four chances fell quickly - all to the former Notts striker Mark Stallard.
He drove wide of the angle with the first and then beyond Kevin Pilkington's right-hand post with the second.
Minutes later Scott Kerr crashed an angled drive against the post, and Stallard failed to get hold of the rebound properly enabling Kevin Pilkington to make an easy save.
Two minutes before half-time a superb run into the Notts penalty area by Lee Frecklington produced Stallard's fourth opportunity which was deflected for a corner.
It proved costly when Notts doubled their lead moments into added time.
A first header by Jason Lee came back off the woodwork and, at close range, the big front man made no mistake with a low header.
By then Lincoln had been reduced to ten men when Jamie Forrester was red-carded in 40 minutes for a foul on Austin McCann.
Lincoln were incensed by this and also that the referee had missed a foul on defender Nat Brown before Lee scored.
Lincoln were faced with an uphill struggle in the second half which became even more difficult when Lawrie Dudfield scored at close range to round off intelligent attacking play by full-back Gary Silk .
Lincoln had Marriott to thank for a smart save to prevent Lee getting a second and then, in a grandstand finish, scored one themselves and almost got a second.
First, substitute Spencer Weir-Daley produced an emphatic finish from six yard to crash the ball past Pilkington.
The keeper then excelled himself by saving a penalty taken by Kerr after a handling offence by Matt Somner. Pilkington also flung himself at Kerr's rebound effort for another heroic stop.
But Notts were full value for the three points.