Huddersfield went close to one that counted when the lively Danny Cadamarteri forced a terrific reaction save from goalkeeper Joe Murphy.
But it was Scunthorpe that struck first in the 19th minute when winger Martyn Woolford celebrated his return to first-team action by thundering a 20-yard effort past goalkeeper Alex Smithies for his fourth goal of the season.
Scunthorpe then suffered a blow when 30-goal leading marksman Gary Hooper was forced to leave the field feeling unwell.
Huddersfield took advantage and were back on level terms in the 26th minute when midfield man Tom Clarke forced home the rebound after a shot from Michael Collins had been blocked by keeper Murphy.
There were no quarters given in a full-blooded derby between these two teams. But after an evenly balanced opening 45 minutes, it was Huddersfield that took charge in the second half, driven forward by midfielder Jim Goodwin who had an excellent game against his former club.
Huddersfield's winner came in the 54th minute when midfield man Gary Roberts exploited a big gap in the middle of the home defence to pick his spot past Murphy with a good finish.
Scunthorpe huffed and puffed in the closing stages but never looked like getting an equaliser and appeared drained in the closing stages with the impact of Sunday's defeat at Wembley against Luton Town in the Johnstone's Paints Trophy Final clearly having an effect.