Lincoln gave themselves a great chance of making the Division Three play off final after smashing home two late goals.
The Red Imps twice looked to have the result beyond doubt, but defensive slip-ups let Scunthorpe back into it.
But the introduction of substitute Simon Yeo in the 73rd minute bought a turn around in the fortunes of the home team.
Yeo took just eight minutes to find the net when he latched onto a Stuart Bimson pass to net with a volley.
Then as Scunthorpe looked to have escaped with just a one-goal defeat Yeo produced the outstanding moment of a thrilling match.
Richard Butcher forced his way to the byline and swept in a cross that Yeo fired first time in to the roof of the net.
The stoppage-time goal was enough to put Lincoln in the driving seat for the second leg at Glanford Park.
The drama began after just 15 minutes when the Scunthrope defence allowed Simon Weaver to sneak in unmarked and head home a free kick from Bimson.
Three minutes later Scunthorpe were left appealing for offside as Paul Mayo got into the box to fire home his first ever senior goal.
Scunthorpe got a goal back from their first corner. Peter Beagrie put the ball across and Alex Calvo-Garcia fired home despite the efforts of Mayo to clear off the line.
Calvo-Garcia was unlucky early in the second half when his long-range shot brought a diving save out of Lincoln keeper Alan Marriott.
But Lincoln went further in front in the 55th minute when excellent work from Dene Cropper set up Paul Smith who shot home from close range.
Scunthorpe suddenly woke up mid way through the second half following the introduction of substitutes Steve Torpey and Paul Dalglish.
Calvo-Garcia got his second goal of the game in the 69th minute and with the Lincoln defence still stunned United were level 60 seconds later.
Nathan Stanton took advantage of hesitation in the Lincoln back four to win the ball on the edge of the box and finished with a 20-yard shot into the bottom corner.
That was the signal for Lincoln manager Keith Alexander to bring on Yeo and the substitute proved his worth to give Lincoln the lead for Wednesday's return clash.