The Tigers took the lead early on. Ray Parlour received the ball down the right and the ex-England international swung in a right-footed cross towards Windass who found space to place the ball past Colin Doyle from 12 yards.
Gary McSheffrey then came close to equalising for the visitors as he set himself up and fired in a right-footed volley from 30 yards forcing keeper Boaz Myhill to scramble back and tip the ball over the bar.
It got worse for the visitors on 34 minutes as Stuart Elliott raced in on goal and Radhi Jaidi took him down just outside the box. The referee adjudged The Tunisian defender to be the last man and sent the Birmingham defender off.
Windass took the resulting free-kick and his curling right-footed effort was inches away from putting Hull further into the lead.
Sam Ricketts then fired in a shot just before the break but his powerful right-footed drive was well saved by Doyle.
The home side came close to grabbing another goal early in the second half when David Livermore fired in a left-footed shot from 25 yards which Doyle managed to touch onto and over the crossbar.
Hull then did score a second on 57 minutes via the penalty spot after Nicky Forster had been brought down by Martin Taylor on the right-hand side of the area. Windass stepped up to take the penalty and coolly slotted the ball past Doyle to score his and Hull's second of the game.
Windass had a chance to complete his hat-trick towards the end of the game when Livermore sent him through on goal, but keeper Doyle did well to save the veteran striker's close-range effort.