The Iron ran out 3-2 winners at home to Cardiff City in their penultimate home Championship fixture of the season.
After a fairly quiet first half, the Bluebirds went ahead through Jimmy Floyd Hasselbaink just prior to half-time.
United soon hit back though, with two goals in four minutes from Paul Hayes and Kevan Hurst putting them in the ascendancy.
They were pegged back on 59 minutes however, thanks to Joe Ledley's strike.
Scunthorpe were to win it though with their third shot on goal of the second period, through a Hayes penalty two minutes into four of stoppage time.
The hosts entered the match making three changes from the team which was sunk at Crystal Palace last week.
Jack Cork replaced Grant McCann in the centre of midfield, while Hurst came in for Ian Morris on the flanks.
Hayes was also re-introduced back into the first team to replace Geoff Horsfield.
United had their first chanced of the game on four minutes, when Izzy Iriekpen - wearing the captain's armband -drilled a half-volleyed effort wide of Peter Enckelman's bottom left-hand post.
Ten minutes later, the visiting team had their first chance of the afternoon when Aaron Ramsey found space on the edge of the 18-yard box to fire in a low strike, which Joe Murphy tipped wide of his bottom right-hand post.
Then, just a few moments later, Glenn Loovens drove wide from distance after a corner was only half-cleared.
The game had opened in a competitive manner, even if chances were limited in the opening period.
Play was drifting from end to end, and both defences were well on top - until the 45th minute when Hasselbaink opened the scoring.
The lively Ledley advanced down the left flank and sent in a low cross for the ex-Leeds and Chelsea man to drive home low to Murphy's right from 15 yards.
He was afforded too much time to pick his spot. As a result, United were a goal down at half-time.
Scunthorpe made a switch at the interval, with Morris coming on for Jim Goodwin. The Republic of Ireland U21 international was deployed in a central midfield position as the hosts searched for a way back into the game.
City had a great chance to double their advantage within a minute of the second half kick-off, when Hasslebaink fired against the post from 12 yards. He then blazed well over three minutes later as the visitors continued to threaten.
The Iron levelled the scores on 52 minutes when Hayes connected with Morris' corner from the right to flick home past Enckelman.
It was his fourth goal of the season, and he was to play an active role in his side's next chance - which also led to them taking the lead.
Feeling confident, he craftily played through Hurst - who had plenty of time to place a low effort past Enckelman from 12 yards. It was a well-worked goal - and a monkey off the back of the former Sheffield United man as he celebrated his first strike in claret and blue.
On 59 minutes though, the visitors hauled their way back into the game through Ledley - who struck a low effort past Murphy from 20 yards in front of the visiting support from Wales.
At this stage it was the Bluebirds who looked most likely to go ahead again, as most of the play was to be found in the Iron's half. The zest which United had after going ahead had disappeared. Nevertheless, the visitors still weren't really testing Murphy.
There was another Scunthorpe change on 75 minutes when Peter Winn came on for Paterson in attack. He would play wide on the left as the home side seeked some fresh creativity going forward.
They were then forced into another alteration with six minutes left as Ben May replaced Jonathan Forte.
As the clock ticked down though there were no more real chances for either side, and it looked like the game was going to end a draw - until Marcus Williams' run into the penalty area was halted by Loovens.
Referee Phil Joslin judged him to have been fouled, and Hayes stepped up to send the ball past Enckelman to his right - as the goalkeeper dived the wrong way.
And that is how it stayed as United recorded their first win in over a month.
Nigel Adkins' side are next in action on Saturday when they visit promotion-chasing Watford.
Sponsors' man of the match: Paul Hayes.
Iron Bar man of the match: Jack Cork.
Attendance: 4,727 (497 away).
