The Sky Blues were left to rue a number of missed chances as they slipped deeper into relegation trouble, they have now gone nine games without a win.
- Scunthorpe United 1-0 Coventry City: As it happened
- Championship League Table
Instead it was fellow strugglers Scunthorpe who overcame the loss through injury of goalkeeper Joe Murphy to notch up their first win in six.
Coventry had the edge in the early stages with Leon Best twice squandering clear-cut chances.
First he saw a weak angled shot easily saved by Murphy, with team-mate Clinton Morrison waiting unmarked in the middle in front of goal.
Then he raced free into the box again only to see his first shot blocked away by defender Rob Jones and a follow-up effort scrambled off the line by Murphy, who hurt himself in the process and had to be stretchered off.
It was Scunthorpe who then began to get going, after Josh Lillis had replaced the stricken Murphy, with winger Martyn Woolford forcing a flying save from keeper Kieran Westwood with a good header.
They took the lead on the half hour when leading marksman Hooper broke clear from the halfway to produce a clinical finish from the edge of the box past Westwood for his seventh goal of the season.
In a defence-dominated second half, striker Paul Hayes was just a whisker away from making it 2-0 to Scunthorpe with a cracking effort that flashed just wide of the far post, following more good work by Hooper.
Substitute Gary Madine had a great chance to snatch a late equaliser for the visitors when he blazed over from close range with the goal seemingly at his mercy after Scunthorpe had failed to deal with a free-kick into their area.
Loanee Madine then suffered further agony as he placed a far-post header wide of target from six yards, as the home side held on for a valuable win.