The hosts took the lead after 19 minutes when Martyn Woolford combined well with Grant McCann and Joseph Mills to smash in his effort from the left-hand side of the area in spectacular fashion.
Huddersfield were back on level terms seven minutes later when Tom Clarke fired home after Joe Murphy had parried Gary Roberts' effort into his path.
Scunthorpe came out much stronger in the opening exchanges of the second period and came close to going ahead once more when Sam Togwell fired a shot inches wide.
But the visitors were ahead 10 minutes into the half when Roberts slid the ball past Murphy from just inside the area.
The hosts looked to push forward in search of an equaliser as the half went on but Terriers goalkeeper Alex Smithies was rarely tested as Huddersfield held on for their third win in four games.