It was Windass who opened the scoring after just six minutes when he curled in a low free-kick from the edge of the box.
But that was as good as it got for the Bantams in the first-half as 40-year-old former Valley Parade favourite Peter Beagrie threatened to spoil the party. He equalised from the penalty spot on 12 minutes after referee Mr Singh ruled that Matthew Sparrow had been felled in the box.
The evergreen wideman then turned provider on the half-hour mark. He teased City full-back Darren Holloway before putting in a sensational cross that was finished by Richard Hinds with a flying header.
The Bantams had totally lost their way and manager Colin Todd rang the changes at the break, throwing on Ben Muirhead and giving Craig Bentham his debut.
But it was that man Windass who turned the game on its head ten minutes into the second half. Bentham's cross found its way to Lewis Emanuel on the right-hand side of the area and he drilled the ball across the six-yard box where Windass was on hand to sidefoot in.
Just a minute later City had the lead. Muirhead sprinted down the right and his low ball found Marc Bridge-Wilkinson sliding in at the far post.
Before Scunthorpe had time to recover Windass was celebrating his hat-trick.
He controlled Aaron Wilbraham's flick-on with his chest before cutting inside and claiming his 20th goal of the campaign, considerably easing Bradford's relegation fears.