After a rather dull first half, the game roared to life from a Wednesday perspective at least as Hooper struck twice in the first five minutes of the second period.
The Owls were rather comfortable but had a scare with ten minutes ago when Leeds scored while the hosts were making a substitution, only to see the goal chalked off after consultation between officials.
Wednesday had the game's first real chance. Hooper met Jack Hunt's cross off balance and headed over from six yards out.
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The hosts dominated the ball for the first 20 minutes, happy to stay in possession and wait for the opportunity to attack with menace.
And they looked strong on the break. Barry Bannan cut out a pass on half way and launched forward before clipping a cross which just failed to reach Fernando Forestieri at the back post.
Leeds on the other hand looked nervous, giving the ball away cheaply and inviting pressure on.
But for all Wednesday's good possession, it was the hosts who should have been ahead by the mid-point of the half.
First, Stuart Dallas drilled in a low cross only for a slight deflection to take it away from Lewis Cook who was poised to strike inside the six yard box.
And Lewis Price should have done better with Dallas' low shot after a surging run but he quickly atoned and he sprung up to block Lewis Cook's follow-up from point blank range.
Wednesday went flat as the half wore on and Leeds began to see much more of the ball.
For long periods, the hosts struggled for meaningful possession.
It made for a rather dull affair with neither side really troubling the opposition keeper.
Cook clipped a shot just past the far post after Glenn Loovens was robbed of the ball while Forestieri tested Marco Silvestri with a rasping drive from 20 yards which was well held by the Leeds keeper.
The visitors had the last say of the half when Souleymane Doukara cut inside and fired low, with Price getting down well.
They may have finished the first half slowly but Wednesday roared out of the blocks after the break.
Forestieri tested Silvestri's alertness with a shot from the corner of the box which the Italian keeper tipped wide at his near post.
And from the subsequent corner, Wednesday took the lead.
The ball was tossed into the area, leading to an almighty goalmouth scramble with Hooper forcing the ball over the line from a yard out.
By the 50th minute, Wednesday were two up.
Forestieri again went for goal from distance with Silvestri failing to claim, allowing Hooper to dart in and tap home.
Wednesday looked incredibly comfortable on their lead, happy to keep possession and frustrate Leeds.
Forestieri took every opportunity to shoot, drawing a more convincing save from Silvestri from the corner of the box before smashing just wide from 25 yards.
Leeds showed only occasional flashes of danger to suggest Wednesday would have more comfort with a third goal.
Forestieri was robbed of the ball on half way with Dallas feeding Doukara who lashed a shot just wide of the near post.
Then came the farcical scenes with ten minutes to go.
Wednesday were making a substitution with Lucas Joao replacing Forestieri but as they were doing so, referee Anthony Taylor waved Leeds on to take a free kick which Liam Cooper turned in from close range.
The hosts protested wildly and, after consulting his fourth official, the referee overturned the goaal and sent Leeds back to take their free kick.
The visitors went close from their second attempt with Daniel Pudil heading off the line.
Leeds attempted to apply the pressure late on but struggled for opportunities.
Substitute Mirco Antenucci curled wide from inside the box while Dallas scuffed an effort on target which Price claimed easily.
But Wednesday held firm to move to 13 games unbeaten at Hillsborough and up to fifth in the Championship before the afternoon's fixtures kicked off.
Wednesday: Price, Hunt, Sasso, Loovens, Pudil, Wallace (Helan 83), Hutchinson, Lee, Bannan, Forestieri (Joao 78), Hooper (Semedo 87). Subs not used: Dawson, Palmer, Sougou, Nuhiu, Joao.
Leeds: Silvestri, Wootton, Bellusci, Cooper, Taylor, Dallas, Bridcutt, Murphy (Antenucci 75), Carayol (Mowatt 70), Cook, Doukara. Subs not used: Peacock-Farrell, Bamba, Erwin, Adeyemi, Coyle.
Referee: Anthony Taylor (Cheshire)