It was little more than Scunthorpe deserved after creating the better openings throughout the match but QPR were left ruing a missed chance from Kaspars Gorkss at the start of the second half.
The win extended Scunthorpe's unbeaten league run to four matches while QPR caretaker manager Mick Harford will be keen to arrest his side's worrying decline.
Scunthorpe were unchanged from the side that beat Sheffield Wednesday in midweek and they almost went ahead after only four minutes.
Hooper latched onto a ball in the box and his shot was parried by QPR goalkeeper Carl Ikeme into the path of Paul Hayes who was unable to direct his effort on target.
QPR eventually began to find their rhythm and Adel Taarabt cut inside from the left before firing a shot just wide of the post.
Akos Buzsaky sent a 25-yard effort over the bar before the dangerous Taarabt brought a save out of Joe Murphy in the Scunthorpe goal.
Moments later Scunthorpe's Sam Togwell won the ball in midfield and tried an ambitious lob which went just over with Ikeme scrambling.
With 24 minutes gone QPR thought they had taken the lead when on-loan Arsenal man Jay Simpson rounded Murphy and finished well but the linesman had his flag up for offside.
Both teams were pressing in search of the lead and Scunthorpe should have gone in front when Rob Jones met a lofted ball into the box, only to head straight at Ikeme.
With half-time approaching Togwell volleyed over from the edge of the box when he perhaps should have done better.
QPR immediately set about seizing the initiative after the break and should have been in front four minutes after half-time but Gorkss headed over from close range.
Rowan Vine then squandered another good chance for the home side before Simpson forced Murphy into a save.
Scunthorpe almost made QPR pay for their profligacy when Togwell's long throw fell to Hooper who turned well before seeing his shot parried away by the alert Ikeme.
Four minutes later Ikeme thwarted Scunthorpe once again when he made a good save to keep out Hayes' smart volley.
With 68 minutes gone Hooper had the visiting fans in raptures when he headed home only to see the goal ruled out for a foul on Matthew Connolly.
However, six minutes later Hooper got past his marker before delivering a cross from the right into the path of Thompson who controlled well before slotting home from six yards.
Simpson headed wide as QPR pressed late on but they were unable to find a way back into the match.