The 22-year-old's inspired performance helped the Iron build a five-point cushion over the relegation zone and ended a run of three successive defeats.
Iron boss Nigel Adkins had hammered home the importance of a positive attitude from his players in his programme notes and got the desired response within 19 minutes.
After edging the opening exchanges, Hooper netted his 14th league goal of the campaign as he forced the ball over the line from close range.
The offside flag denied him a quick-fire brace but 10 minutes into the second half his super turn and shot doubled Scunthorpe's advantage to allay fears of a second relegation in three years.
Hooper secured the victory, and his treble, in the 70th minute after superbly rounding City goalkeeper Stephen Henderson and slotting into an empty net.
Scunthorpe headed into the game boosted by the return of Marcus Williams and Kenny Milne in place of Jim McNulty and Michael Raynes, who dropped out of the starting XI and the squad altogether.
City caretaker Keith Millen's only change to the side that grabbed a last-gasp winner against Swansea was enforced, as he brought Christian Ribeiro in for the injured Jamal Campbell-Ryce.
Neither side managed to get a foothold of the game at the start, with defensive lapses allowing chances at either end.
As the half wore on Scunthorpe began to push forward in numbers, with Martyn Woolford twice denied by keeper Henderson in the 14th minute.
And the home side made their pressure count five minutes later when Garry Thompson's whipped right-wing cross found Hooper in the six-yard box, who, despite initially miscontrolling the ball, managed to bumble home.
The goal boosted the home side who thought they had doubled their lead through Hooper's second of the game, only for the linesman to adjudge the striker offside.
At this stage the City goal was under siege and only the bar prevented Woolford from extending Scunthorpe's advantage, after Paul Hayes' neat pull back in the 29th minute.
The visitors weathered the storm for the remainder of the first half, but could only prevent the Iron onslaught for 10 minutes after the restart.
Hooper showed skill and poise that belied the Championship to turn on a sixpence and curl the ball low into the far corner from an awkward angle.
"We are staying up" rang around Glanford Park and the chorus grew louder in the 70th minute when Hooper secured his first hat-trick of the season by smartly rounding Henderson and slotting home.
The undoubted man of the match came off to a standing ovation four minutes later, leaving the team with the worst defensive record in the division to round off a superb victory with a clean sheet.