The Owls had lost their last two games, but Hooper's first-half brace, and a fine volley from Kieran Lee late on, will help vanquish the memories of last weekend's Steel City derby defeat with three points against another Yorkshire rival.
Leeds started much the brighter and had the first clear opening of the match on 15 minutes when Samuel Saiz dropped the ball onto the head of Ezgjan Alioski, whose back-post effort was tame and into the side-netting.
Hooper was much more potent when he got his chance 10 minutes later, reacting quickest at the back post to prod past Leeds goalkeeper Felix Wiedwald.
It was from another second ball that Hooper doubled Wednesday's lead shortly before the break, with Steven Fletcher heading across goal for his strike partner to apply another close-range finish for his ninth goal in as many games against the Whites.
The Owls deserved their two-goal half-time cushion, and it should have been more because Lee had a 31st-minute goal incorrectly ruled out for offside, and Fletcher missed a simple header from inside eight yards.
Wednesday started the second period sloppily, though, and were lucky not to see their deficit halved on 47 minutes when Pierre-Michel Lasogga pounced on a mistake from Joost van Aken and shot against the outside of the post.
That proved to be Wednesday's only genuine scare as they soon regained control of proceedings, and they nearly grabbed a third when Barry Bannan slid in Hooper for a shot which was well blocked by Wiedwald.
Bannan went closer himself when he struck the post from the edge of the box on 81 minutes, but it was Lee who eventually put the result to bed with a sweetly-struck volley into the bottom corner, after a casual Eunan O'Kane clearance fell to him 22 yards out.
Hooper was denied a hat-trick by a combination of Wiedwald and the crossbar in stoppage time, after he had latched onto a Jordan Rhodes knockdown, but the three-goal victory is enough to take Wednesday into the top half of the Championship on goal difference.
Leeds fall to fifth in the table and have now lost three of their last four matches, although all of those defeats have been away from home.