The Red Imps found it hard going early on and went a goal behind after only eight minutes, but they fought back well and took the points with three late goals to climb up to 14th in the League Two table.
Lincoln had a let-off after only six minutes when Danny Thomas raced clear down the left and set up Michael Symes, but the striker shot well wide from a good position.
Two minutes later Lincoln were again caught out by a ball over the top when Terry Dunfield sent Gareth Evans clear.
City keeper Alan Marriott raced off his line, but Evans took the ball round him and slipped the ball into the empty net.
Lincoln's defence looked fragile and they fell apart again in the 18th minute when a deep cross from Sean Hessey picked out Francis Green, but the striker volleyed his first-time shot over.
Lincoln slowly began to get into the game and went close in the 33rd minute when a low shot from Jamie Forrester deflected off Izak Reid forcing Jonny Brain to save on the line.
Brain made a superb double save four minutes later to keep out Mark Stallard, but suffered a cut head and had to be replaced by Tommy Lee.
Lincoln had a great chance to level in the 53rd minute when a shot from Stallard came back off the bar, but Lenell John-Lewis shot wide with the goal at his mercy.
City took complete control after Macclesfield skipper Dunfield limped off with an ankle injury. Forrester sent a header wide after being left unmarked on the edge of the six-yard box.
Forrester then shot straight against his own team-mate Stallard from a good position.
Lincoln eventually equalised in the 72nd minute when Forrester's cross found Stallard. The striker's header came back off the post, but John-Lewis put the rebound into the net.
John-Lewis then forced his way down the left before crossing for Forrester to fire home.
Lincoln added a third in stoppage time when 40-yard pass from John-Lewis put sub Dany N'Guessan clear and he finished with a shot which went in at the far post.