The Iron did well to overcome the early loss of goalkeeper Joe Murphy, and despite handful of scares were able to protect their lead and leapfrog the Sky Blues in the Championship standings.
Having rescued a point against Leicester last weekend with a last-gasp equaliser, Scunthorpe started crisply and Cliff Byrne flashed a header just wide after five minutes.
It was Coventry, though, who should have twice taken the lead inside 10 minutes, with Republic of Ireland striker Leon Best culpable on both occasions.
The first chance came when Best found himself one-on-one with Murphy after a slip by Rob Jones, but he fired straight at the goalkeeper rather than squaring to Clinton Morrison.
Then, just 30 seconds later, Best found himself in a similar position after being sent clear by Aron Gunnarsson and, after his first effort was blocked by Jones, his second was superbly saved by Murphy.
The keeper's afternoon ended there, though, as his knee crashed into the post as he saved Best's drive, a collision that saw him leave the field on a stretcher.
After a six-minute delay, replacement goalkeeper Josh Lillis had to make a fine save from Morrison's strike, while at the other end Kieren Westwood produced an impressive one-handed save to keep out a Martyn Woolford header.
A goal did arrive 30 minutes in, with Hooper lashing home his seventh of the season.
City defender Richard Wood was drawn out of position, Paul Hayes took advantage and backheeled a loose ball into the space vacated by Wood and a rampant Hooper barely looked up as he drilled home from the edge of the area.
Grant McCann went close to making it two with a low free-kick before the half-time whistle, and his side continued to impress after the restart, with Hooper not giving the Coventry defence any breathing space.
Coventry appeared much more focused after the resumption, but were unable to force their way through a Scunthorpe defence which was now looking more solid after its early wobbles.
Woolford and Martin O'Connor both took aim from distance for the home side as they tried to extend their lead, something Hayes should have done with 13 minutes remaining.
He again linked up with Hooper, with his strike partner's backheel playing him into the area, but Hayes could only drive his angled shot across the face of Westwood's goal.
Hayes could have been punished for his generosity, but City sub Gary Madine twice failed to convert from six yards in the closing minutes, while the visitors also unsuccessfully appealed for a penalty after the ball appeared to strike David Mirfin's hand.