Lee Novak's 89th minute strike was enough to hand Town their first win in four and keep up with MK Dons in the race for fourth place in npower League 1.
The visitors had arguably the better of the first half and went close to opening the scoring twice when Ian Bennett saved well from Robbie Gibbons and Bobby Grant smashed the upright with a superb free-kick.
The second 45 saw Town dominant territorially, but again the Iron went close to scoring when Jimmy Ryan clipped the outside of the post. The game looked to be heading for a draw, however, with one minute of normally time left to play Lee Novak raced clear and finished well.
Simon Grayson made one change to his team for the penultimate home game of the regular season with Lee Novak returning from injury to take the place of Danny Ward, as Town returned to a 4-4-2 formation.
Another notable inclusion was that of Chris Atkinson who was named amongst the substitutes for the first time this season.
Town's right side partnership of Jack Hunt and Scott Arfield started the game well and created the first chance of the game when the latter got in behind Jamie Reckord and forced Cliff Byrne to clear from inside his own six yard box with a well-directed cross.
As the Terriers good start continued United's central midfielder Sam Togwell forced his own 'keeper into his first save of the game when he made a good last ditch tackle to deny Lee Novak, however, in the process he sent the ball towards his own goal and into the arms of the diving Sam Slocombe.
Bobby Grant was making his first appearance since his return from loan for the Iron and did brilliantly in the 11th minute to hold off the attentions of Peter Clarke and release Andy Barcham. The winger struggled to bring the ball under control, but thankfully for him Robbie Gibbons was following up and forced Ian Bennett into a fantastic one handed save. From the resulting corner former Terrier David Mirfin rose highest, but nodded his header wide.
With 15 minutes on the clock Town split the Iron open down their right hand side when good interplay between Diego Arismendi and Gary Roberts freed Novak. The striker immediately fed the ball back to Roberts who was faced with a one on one with Slocombe; the winger had options with Scott Arfield on his inside, but he chose to go alone and fired tamely at the Iron's 'keeper.
Town's defence looked comfortable with the attacking threat that the Iron posed, however, they were within a couple of inches of going behind in the 27th minute when Grant smashed a free-kick, following Calum Woods' foul on Togwell, from 25 yards against the upright.
BOOKING - Town's Uruguayan Diego Arismendi received the first caution of the game with ten minutes remaining of the first-half when he scissor tackled Mark Duffy.
As the half drew to a close a clever piece of individual play from Jack Hunt saw him skip past Andy Barcham and fire just over Sam Slocombe's goal, as the Terriers tried to force the 'keeper into his first meaningful save of the half.
HALF-TIME - TOWN 0 UNITED 0
The first ten minutes of the half passed by with little incident before Roberts showed Cliff Byrne a clean set of heels from a throw-in and released Robinson, whose first touch let him down as he burst into the area.
Jordan Rhodes had been starved of the ball during the first hour of the game, however, in the 60th minute Arfield slipped the ball through to the Scotsman, but in uncharacteristic fashion he sliced the ball wide and into the Fantastic Media Stand.
SUB - Town's inability to break down a stubborn Iron defence forced Simon Grayson into his first change of the game replacing Diego Arismendi with Danny Ward - the change saw Arfield move into the centre of midfield alongside Anton Robinson.
A moment to forget for Gary Roberts in the 67th minute almost handed the visitors the opening goal. The winger held onto the ball for far too long on the edge of his area and saw it taken off him by Grant; he proceeded in skipping past Clarke before passing to Jimmy Ryan, who struck the upright from 12 yards.
The Terriers forced Slocombe into his first save of the half with twenty minutes of the half remaining when substitute Ward stepped inside Reckord and fired low into the arms of the stopper.
Ward's shot seemed to spark the Terriers into life and in the 77th minute they thought they had opened the scoring when Jordan Rhodes slid the ball past Slocombe. The move started with Arfield - who was becoming ever more influential from the centre of the park - and ended with him when he dragged his effort into the path of Rhodes, who turned sharply and prodded home, but was adjudged to have been offside.
The visitors then should have opened the scoring when Benno spilled Gibbons' shot into the direction of the onrushing Grant who smashed the rebound against the bar and out of play.
BOOKING - Sean Morrison received Town's second yellow card of the game with 12 minutes left in the game for an act of dispute.
SUB - Academy graduate Chris Atkinson made his first appearance of the season with ten minutes remaining at the expense of Robinson.
SUB - Danny Ward was the recipient of Town's third yellow after throwing the ball away in anger.
With only a few minutes remaining Town resorted to knocking the ball long and it almost paid off when Clarke's knock down fell in the direction of Ward, who hit a rasping volley just over Slocombe's cross bar.
GOAL - With one minute remaining of normal time the Terriers opened the scoring when Lee Novak raced clear and slotted underneath the advancing Slocombe. Gary Roberts collected the assist with a neat through ball which fell kindly for Novak and although the Iron's 'keeper got something on the ball, he couldn't prevent it going in the back of his net.
SUBS - Both managers made a change in the first minute of injury time with Conor Jennings replacing Sam Togwell and Tom Clarke replacing Jordan Rhodes for the Terriers.
FULL TIME - HUDDERSFIELD TOWN 1 SCUNTHORPE UNITED 0
Town's team (4-4-2):
Ian Bennett; Calum Woods, Peter Clarke (c), Sean Morrison, Jack Hunt; Gary Roberts, Diego Arismendi (Danny Ward 62), Anton Robinson (Chris Atkinson 80), Scott Arfield; Jordan Rhodes (Tom Clark 90), Lee Novak
Nick Colgan, Danny Cadamarteri
Bookings Town: Arismendi 36, Morrison 78, Ward 82,