It was Bruce's 100th game in charge of Villa and only the fifth time they have lost at home under his control.
Villa were sadly out of touch against an eager Wednesday side who were always prepared to pressurise.
Following an indifferent first half, Wednesday were well worth their away success with some skilful attacking play.
The visitors were often the more dangerous in a goalless first half when the likes of Marco da Silva and Adam Reach posed problems for Villa's suspect defence.
Da Silva put them on the winning path with a 49th minute goal and John McGinn produced a spectacular 54th minute equaliser but Steven Fletcher sealed the points for the Owls in the 66th minute.
The indifferent form of Jonathan Kodjia and Tammy Abraham is a worry, while Jack Grealish struggled to open up Wednesday's defence.
To their credit Wednesday were always prepared to counter-attack and Barry Bannan was the mastermind behind most of their moves.
This was evident in the first half when Wednesday were often the more dangerous side and this gave them the confidence to hit Villa four minutes into the second half.
A shot by Adam Reach was blocked into the path of Da Silva who hammered home a raking dive to the right of the helpless Orjan Nyland.
In the 54th minute Villa were back in the game when a headed clearance found the unmarked McGinn who slammed in a 25-yard shot on the volley which cannoned off the bar and into the net.
Villa's hopes of taking control, however, quickly disappeared when Joey Pelupessy advanced down the right to produce a high cross which found the unmarked Fletcher to head home the winner.
There was some late attacking play from Villa but Wednesday's stalwart defence held firm to take the points which lifted them over their opponents in the league.