Rene Howe's second half penalty condemned Macclesfield to a first defeat in four League outings in a game they dominated for long periods.
Home keeper Jon Brain was judged to have brought down Lincoln substitute Jamie Clarke with 20 minutes to go and Howe stepped up to give rookie manager Chris Sutton his first away win as Imps boss.
Howe could have scored in the ninth minute after a mix-up in the Macc defence allowed the former Morecambe man to race clear but Brain managed to get enough of a hand to his drive across the face of goal to push it around the post.
In a slow start the away side saw more of the ball but after the first ten minutes the first half belonged to the Silkmen.John Rooney had Macc's first effort - hitting an ambitious 25 yard volley well over and out of the ground, although his brother Wayne would have been hard pushed to hit the target from such range.
Colin Daniel went closer for Macc on 17 minutes hitting a vicious drive from the corner of the area which whisted inches wide of the far post and had Imps keeper Rob Burch scrambling across his goal.
Nat Brown headed over from a Lee Bell corner as Macc took the game to the visitors with the majority of their play coming down the right as Emile Sinclair's pace caused left back Aaron Brown problem after problem.
The Macc fans were on their feet celebrating prematurely on 31 minutes when Daniel squeezed out a cross from the byline which was half-cleared out to Rooney who expertly darted between two defenders before slotting past Burch but unfortunatelywide of the post.
The young forward was in the action again soon after and was getting closer, this time he picked the ball up in space 25 yards out before unleashing a curling, dipping effort which had Burch back-peddling and clipped the top of the bar.
John Rooney - Was at the centre of all Macc created and went close on a number of occasions
After dominating for the last half hour of the half, Macc had a huge let off just before the break when Lincoln skipper Stefan Oakes collected the ball in acres of space just ten yards out and after taking time to pick his spot miss-kicked well wide.
Macc failed to come out after the interval as dominant as before and for the first 15 minutes of the second period had just Izak Reid's wayward 20 yard shot to show for their efforts.
Daniel's cross was blocked behind for a corner by what appeared to be the arm of a visiting defender but the claims were waved away.
The referee did find his whistle ten minutes later though to award the visitors with a spot kick against the run of play.A contested Lincoln free kick on halfway was hit long into the box and after Richard Butcher nodded the ball down Jamie Clarke got to the ball first and went down as Brain also came out for the ball.Howe sent Brain the wrong way to tuck away the spot kick for his second of the season.
Hamza Bencherif and Shaun Brisley both went into the book as a frustrated Macc struggled to get back into a game they felt they should have been leading.
Matthew Tipton and Ricky Sappleton were thrown on towards the end and loanee Sappleton went close a few times in his 14 minutes on the pitch.His low drive was blocked by Burch's legs and when the ball came back to him his follow-up effort looked to be clearly blocked by an arm in the six yard box but again nothing was given.
Carl Tremarco and Rooney again went close in the last five minutes with shots from outside the box with Lincoln sitting back more and more just trying to run the clock down.
On 89 minutes a diagonal ball into the box found Sappleton leaping high above his man at the far post and his looping head looked to be dropping in but Burch somehow dived back to claw it away.
Four minutes of stoppage time were shown and with the home crowd urging them on, Macc managed to create one more chance.Burch was again there to thwart the Silkmen though as Bencherif hammered a shot from 15 yards which bounced off the legs of the keeper and away to safety.