A Kevin McIntyre penalty in each half gave the Silkmen their sixth win in seven games against a high flying Lincoln side who had previously won four on the spin.
Macclesfield started with Matthew Tipton partnering Matt McNeil up front, with John Murphy left on the bench. Jamie Tolley, back from suspension, was also a substitute. The game was skipper Dave Morley's 250th league start.
Former Silkman Spencer Weir-Daley was on the bench for the Imps, who had Mark Stallard partnering the 14-goal Jamie Forrester in attack.
The visitors had the first shot on target of the game after just 30 seconds - Jeff Hughes' long range free kick stinging the hands of Tommy Lee.
Macc went ahead after just six minutes when the referee gave the first penalty of the afternoon. Matt McNeil chased a long ball forward and after jostling with Shane Nicholson he appealed for handball. The linesman flagged and after a quick consultation the referee pointed to the spot after seeing the offence was in the area. McIntyre stepped up and sent the keeper the wrong way, smashing the ball into the bottom left corner.
McNeil had a chance to double the lead on 12 minutes, but after Martin Bullock's run from the left, he miss-hit his first volleyed chance and then saw his follow-up header headed off the line by Paul Morgan.
Macc's lead wasn't to last long though as the impressive Jeff Hughes scored his sixth goal of the season, thanks to a combination of poor defending and individual skill. Ryan Amoo's deep cross from the right should have been cleared by Carl Regan, but after he missed it, Hughes capitalised with a wonderful turn back inside and shot across into the far corner.
Tipton went close as his shot was deflected just past the post by Morgan and then Morley latched on to a loose ball to hammer a volley straight into the arms of Alan Marriott from the edge of the box.
Good link-up play with the two Macc strikers gave McNeil a great chance after he was found from Alan Navarro's cross but he could only prod the ball at the keeper and it rebounded to safety.
Navarro conceded a free kick on 27 minutes after a poor kick from Tommy Lee, however the young keeper made amends by diving full length to deny Nicholson as he took the kick quickly.
Forrester should have had his 15th of the season from Hughes' corner from the right, however when it looked easier to score he headed wide unchallenged from close range.
Nat Brown was lucky to escape with just a yellow card when he hauled down Tipton as he surged past him as the last man. The resulting free kick was chipped into the box and Tipton volleyed out of the ground from a tight angle.
Macc again went close towards the end of the half when Jordan Hadfield drilled wide and Danny Swailes just couldn't get high enough to meet McIntyre's cross from the left.
The half time whistle went with Macc in some ways unfortunate not to be ahead, but had only found the net from a controversial penalty. Lincoln were looking for the early runs of Forrester, who had already beaten the offside trap on a few occasions, although they offered little apart from the skills of Jeff Hughes.
The Imps came out better after the break with Forrester twice breaking through on goal. First he found himself through down the right channel but fired straight at the chest of the oncoming Lee and then minutes later Morley's error allowed him in, only to shoot too close to the keeper again when he had lots of time.
A good Lincoln move down the right gave Forrester two chances on goal but after his initial shot rebounded back to him his second effort was blocked by Swailes.
Tommy Lee was forced into another great save when he clawed away Ryan Amoo's rising shot after he was picked out in space on the right.
Izak Reid was found by Swailes following a corner, but his shot from the edge of the box was nodded over by Regan when it may have been heading in.
Jeff Hughes was booked for a late challenge on Bullock before Macc were awarded their second spot-kick of the afternoon. A bouncing ball fell to McNeil with his back to goal and he appeared to swing for the ball and fell backwards under Adie Moses challenge. The referee pointed to the spot again amid huge protestations from Lincoln players and fans.
McIntyre went the other way this time to score his fifth penalty of the season and put the home side back in front with 25 minutes to go.
Lincoln pushed forward looking for another goal and forced a string of corners, culminating in a clearance off the line after Amoo shot from the edge of the box.
Navarro nearly added to the lead on 72 minutes. He placed his shot just the wrong side of the post after he was found by Bullock, who was having a better second half in conditions which didn't really suit his game.
Former Macc man Weir-Daley came on for Shane Nicholson and was quickly booked after going in late on Lee, which didn't win him any favours with the home crowd who were already booing him.
John Murphy came on for the last ten minutes to replace Tipton, and then soon after being booked for time wasting Bullock was withdrawn for Tolley.
Lincoln pressed forward towards the end as Macc began to sit deep to hold onto their slender advantage, but the nearest they came to another equaliser was Forrester's shot on the turn which was too close to Lee to cause any problems.
So another game and another three points for the Silkmen - who are beginning to look like they can beat anyone in this division. The only negative point was hearing that many of the other struggling teams had also won, although the victory puts Macc six points clear of rock-bottom Torquay.
Andy Brinkhurst
