Skipper Cliff Byrne was missing from the Iron line-up with a back injury.
Michael Raynes came into the team at right-back and there was a start in midfield for Michael O'Connor who had missed the previous two games with a thigh problem.
Former United defender Jamie McCombe was one of several new summer signings in the Huddersfield line-up.
United suffered an injury blow in the opening minutes when centre back Rob Jones limped off to be replaced by Andrew Wrght. Raynes switched the the middle of the defence.
It was a lack-lustre first half in front of a sparse crowd of just 1,400 at Glanford Park.
Anthony Pilkington produced the first effort at goal for the League One visitors with a snap-shot that was blocked out by keeper Joe Murphy.
At the opposite end, Scunthorpe offered little, though one good move did create an opening on the edge of the box for O'Connor whose well struck shot was blocked away by Peter Clarke before it could test keeper Alex Smithies.
It was a lack-lustre affair in front of a poor crowd.
Huddersfield nearly snatched the lead after 38 minutes when Graham Carey cut into the box from the right to drive in a shot that Murphy was happy to beat away.
Seconds later, Pilkington set up another chance for an unmarked Carey, but he dragged his shot well wide.
It was 41 minutes before Scunthorpe tested visiting keeper Smithies when Josh Wright popped up in the box to get in a header from a good cross from the right by Andy Wright.
As the game entered first half stoppage time, it was Huddersfield who went close again when Joe Garner flashed a header just wide of the far post.
It was Scunthorpe who finally broke the deadlock in the 52nd minute when the visitors lost possession on the halfway line.
Thompson picked up possession and exchanged passes with Chris Dagnall before drilling a left foot shot past Smithies.
That sparked the home side into life and they almost struck again when Jonathan Forte found room on the edge of the box to fire in a shot that Smithies just managed to turn away at the foot of his left-hand post.
Suddenly there was uncertainy in a Huddersfield defence that had looked solid, and McCombe headed an attempted clearance just wide of his own goal.
From the corner that followed, Josh Wright curled the ball in from the left for Dagnall to get in a near post header that was blocked on the line, but Huddersfield could not scramble it away before Michael Raynes applied the finishing touch from point blank range after 61 minutes.
Scunthorpe almost made it 3-0 when a Forte header from a corner beat Smithies, but was headed off the line by full-back Scott Arfield.
Huddersfield were denied a consolation reply 10 minutes from time when Murphy tipped over a 20-yard drive from Anthony Kay.
SCUNTHORPE: Murphy, Raynes, Mirfin, Jones, McNulty, Forte, J Wright, Togwell, O'Connor, Thompson, Dagnall.
HUDDERSFELD: Smithies, Arfield, Naysmith, Gudjonsson, Clarke, McCombe, Roberts, Pilkington, Garner, Kay, Carey.
ATTENDANCE: 1,484 (309 away).