The visitors who carved out all the early chances - and who were also denied by the woodwork.
Scunthorpe enjoyed plenty of first half possession, but were totally lacking in a cutting edge up front.
Their only effort of the opening 45 minutes was a wayward long-range shot from midfield man David Syers that flew over the roof of the stand.
It was Hartlepool who looked more menacing, three times testing Sam Slocombe in the home goal.
First he had to be alert to pluck out an acrobatic header from Christian Burgess. Then he palmed away a low 25-yard effort from midfield man Matthew Dolan and he saved his best until last, reacting well to turn over a well-struck angled effort from Jonathan Franks after he had broken free into the box.
Hartlepool went even closer in the 51st minute with a rasping long-range effort from Andy Monkhouse that took a deflection before rattling the outside of a post.
But it was Scunthorpe who snatched the lead in the 77th minute as Winnall capitalised on a defensive slip to race free into the box and steer a right-foot shot past keeper Scott Flinders for his sixth goal of the season.