Former Scunthorpe midfielder Jim Goodwin scored his first Huddersfield goal to help set up a tense victory.
Town went close early on when Nathan Clarke's header was cleared off the line by Sam Togwell, who later hit the bar for United with a left-foot shot.
Town keeper Alex Smithies saved well from United's top scorer Gary Hooper before Goodwin rose highest to head in Gary Roberts' corner on 65 minutes.
Smithies again denied Hooper before Roberts tapped home to seal the win.
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Booked: Parker, Smithies.
Goals: Goodwin 65, Roberts 90.
Scunthorpe: Murphy, Wright, Byrne, Pearce (Thompson 85), Williams, Sparrow, McCann (Morris 78), Togwell, Woolford (Hayes 73), Hooper, May. Subs Not Used: Lillis, Mirfin.
Booked: Murphy, Sparrow.
Att: 15,228
Ref: Nigel Miller (Durham).
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