The Iron striker had two efforts chalked off before the break, the offside flag twice keeping the home side on level terms, before the woodwork denied Jeff Hughes an opener for Town.
But Scunthorpe broke the deadlock, against the run of play, just before the hour mark. Fleetwood took too long to clear their lines and Winnall's effort cannoned off a red shirt on the way past goalkeeper Scott Davies.
Before that the hosts should have gone ahead, but Sam Slocombe stood tall in the Scunthorpe goal to deny Hughes.
The Iron stopper was having an inspired night, also keeping out Gareth Evans and Antoni Sarcevic before the visitors struck.
From then on Brian Laws' side dug in and defended their lead. Substitute Jamille Matt found the back of the net for Fleetwood but, like Winnall before him, his effort was flagged offside.
Fleetwood threw three strikers into the mix late on but could not break down a resolute defence.
Deon Burton came close to adding a second for the visitors, the substitute sending his shot spinning over the angle having escaped the attentions of Liam Hogan.