Hooper scored twice in the first half to move on to seven goals in as many games, pouncing on captain Tom Lees' flick-on to beat indecisive keeper Felix Wiedwald with a prodded finish to open the scoring after 25 minutes.
Rampant Wednesday then had a goal from Kieran Lee wrongly ruled out for offside, while Steven Fletcher headed wide when Ross Wallace's cross gave him a glorious chance.
The Owls struck again four minutes before the break, Hooper heading into the far corner after strike partner Fletcher rose to guide Liam Palmer's cross into his path.
Leeds improved after the break and a defensive mistake from Joost van Aken presented Pierre-Michel Lasogga with the visitors' best chance, only for the striker to hit the post from 12 yards.
Wednesday continued to impress, Barry Bannan hitting the woodwork at the other end shortly before Lee finally got his goal by smashing in a fine strike from 20 yards.
There was also time for Hooper to smash the bar in search of his hat-trick as victory for the hosts, their first in four games, moves them up to 12th. Promotion-chasing Leeds could have gone second with a win, but instead slip to fifth after a third straight away defeat in the league.