Striker Paddy Madden scored the only goal of a tight game in the 59th minute to lift his side back to second in the table.
In a dour first half it was Scunthorpe who enjoyed most of the pressure, but they rarely threatened a breakthrough.
Burton's main threat came from set pieces and it was from their first corner if the 21st minute that they came closest to a goal.
It reached the far post where Damien McCrory got in a goal-bound header which was headed away by Scunthorpe full-back Marcus Williams.
The home side's first real threat did not come until the 53rd minute when a wind-assisted 40-yard free-kick from Gary McSheffrey dipped just inches over the bar.
Almost immediately they made a double substitution, bringing on striker Paul Hayes and winger Hakeeb Adelukan as manager Russ Wilcox looked for more from his side as an attacking force.
And it produced an instant reaction as Scunthorpe broke the deadlock in the 59th minute when Madden cushioned a brilliant volley from the edge of the box into the rook of the net after Burton had only half cleared a free-kick into the box from McSheffrey.
Scunthorpe should have made it 2-0 in the 75th minute when McSheffrey saw his weak penalty saved by goalkeeper Rob Lainton after he himself had been brought down in the box by full-back Phil Edwards.
It was a lifeline for the visitors but they never threatened an equaliser.