It halted a run of three successive defeats for United who are now five points clear of the bottom three and it was the first defeat in seven games for City since Keith Millen took over as caretaker manager.
The visitors started strongly and goalkeeper Joe Murphy twice came to the home side's rescue in the early stages to deny City the lead.
He did well to block away a fierce effort from Danny Haynes who had pounced on a mistake by full-back Marcus Williams to get free in he box then he scrambled across his line to deny Haynes again, tipping away his glancing header that looked destined to squeeze just inside the far post.
Scunthorpe capitalised on their custodian's good work when the prolific Hooper fired them in front after 18 minutes with his 14th goal of the season, forcing the ball home from close range at the second attempt.
Hooper had the ball in the net again just a few minutes later, only to see his effort ruled out for offside.
He was proving a real handful for the City defence and on the half hour set up a good chance for midfield man Martyn Woolford who rattled the bar with a left foot effort.
The second goal that Scunthorpe needed came in the 55th minute and it was that man Hooper who struck again with a shot on the turn into the bottom far corner of the net after City had failed to deal with a free-kick in their box.
It was nearly 3-0 when Paul Hayes found space just inside the box, but his shot was well blocked away by Stephen Henderson.
Scunthorpe's third did arrive in the 70th minute when Hayes sent Hooper racing clear of a poor City defence as he rounded Henderson to complete his hat-trick.