United, without an away league win since December 18, were on the back foot right from the start after conceding a goal in 30 seconds.
Francis Green hit a 40-yard pass over the Iron defence and Simon Yeo controlled the ball superbly before cracking home a low left-foot shot from the edge of the box.
Lincoln almost went further in front in the fourth minute when visiting keeper Paul Musselwhite did well to keep out a header from Ben Futcher.
The Imps kept up the pressure and Green was denied again by Musselwhite when he attempted to chip the keeper.
Scunthorpe struggled to create chances but went close in the 32nd minute. A corner from Ian Baraclough was headed down by Steve Torpey, but Andy Keogh was just unable to connect.
Musselwhite then brought off a tremendous one-handed save to keep out a 25-yard free-kick from Kevin Sandwith.
United put on plenty of pressure in the second half, but could not force a way through.
They won a string of corners but Lincoln's defence held out. Baraclough went close when he blasted a 20-yard shot through a crowd of players, but City keeper Alan Marriott saved well at the foot of his post.
Lincoln clinched their third consecutive victory with a classic goal from Gary Taylor-Fletcher. Green put the striker clear and he lobbed the keeper from just inside the box.
Scunthorpe continued to push forward after the goal but it was too late.
Baraclough fired a long-range free-kick over the defensive wall, but Marriott was well placed to save.
Six minutes from time Scunthorpe almost grabbed a consolation goal when substitute Paul Hayes had Marriott beaten with a close-range effort, but former United defender Jamie McCombe cleared off the line.