Adam Reach set the visitors on their way with the opening goal after only 19 seconds and fellow former Middlesbrough man Jordan Rhodes made it two before the break.
Chris Samba's last-minute reply was too little, too late for Villa, who also lost John Terry to injury.
Wednesday’s delighted boss Carlos Carvalhal has recently suffered criticism but he feels the recent improvement vindicates his optimism.
He said: “We did really well as Villa found it difficult to create chances. We took advantage of our early goal and could have finished the game.
“But that would have been unfair to Villa because of the way they played in the second half.
“I am happy with our performance as we have played well in the last three games.
“We know we can challenge the play-offs as the quality of our play should ensure we are challenging at the end of the season.”
Steve Bruce's side went into the game with six wins from their previous eight games, but never recovered from their nightmare start.
Straight from the kick off Ross Wallace gained possession to set up Reach, who produced a stunning left-footed swerving shot from fully 30 yards which flew into the top corner of the net.
With seven clean sheets in their previous 10 games it was a shock to the system for Villa as they struggled to assert their authority.
Wednesday had their tails up thanks to the early goal and produced several promising attacks, often engineered by Barry Bannan.
Villa suffered another blow in the 21st minute when skipper Terry was forced to limp out of the game with a leg injury, to be replaced by Samba.
It proved a crucial moment as Wednesday steamed further ahead within a minute of Terry's premature departure.
Bannan cleverly played a one-two with Rhodes to cut through a defence clearly weakened by the departure of the former England international and Rhodes took full advantage by slipping the ball home unchallenged.
It was the first time since April 2016 that the striker, who ended a 25-game goal drought against Millwall last time out, had scored in successive matches.
Villa frustration grew as they struggled to find some attacking rhythm against a Wednesday side which continued to gaind in confidence.
Five minutes before the break a disgruntled Robert Snodgrass, an injury doubt before the game, was replaced by teenager Callum O'Hare.
Villa were far more positive in the second half following the introduction of Jack Grealish, but were lucky not to concede a third when substitute Liam Palmer missed an open goal.
Samba's last-gasp strike finally gave Villa something to cheer, but there was never any chance of a comeback.