A Jermaine Johnson inspiried Wednesday side inflicted a 3-2 defeat on Rovers at Hillsborough.
It had started well for Gary Bowyer's side when Jordan Rhodes notched his 24th of the campaign from the penalty spot after David Dunn had been fouled on 12 minutes.
But quick feet from Johnson soon saw the home side level, the midfielder outpacing Rovers to fire home on 20 minutes.
Then on 35 minutes the Owls were in front, Leroy Lita taking full advantage of a generous penalty decision to fire home from 12 yards.
The second half saw Rovers camped in Wednesday's half for lengthy periods, eventually the pressure told when Scott Dann headed Rovers level with 19 minutes to go.
However it was Johnson who would prove to be a thorn once more, lashing an unstoppable 25-yard drive into the far corner of the goals to give the Sheffield club all three points.
The result sees Rovers drop into the bottom three, with two home games coming up nothing but six points will do.
Following Rovers' 3-0 Easter Monday loss at Cardiff City, manager Gary Bowyer made six changes for the match against Sheffield Wednesday.
With Jake Kean ruled out for the remainder of the season, Grzegorz Sandomierski was handed his first Rovers start in goal.
Also coming back into the starting eleven were Cameron Stewart, Lee Williamson, Jason Lowe, David Dunn and Jordan Rhodes.
Morten Gamst Pedersen and Colin Kazim-Richards dropped to the bench, Leon Best missed out with a slight calf injury, whilst David Bentley and Danny Murphy didn't make the 18-man squad.
It was a bright start from Rovers in the bright sunshine at Hillsborough with Bowyer's side taking the lead inside 12 minutes.
A Jason Lowe ball foward saw Jordan Rhodes out-muscle Miguel Llera to race into the box, Wednesday 'keeper Chris Kirkland denyed Rhodes but as the rebound fell to David Dunn the stopper brought down Dunn as he attempted to go around him. Referee Roger East had no hesitation in pointing to the penalty spot.
Jordan Rhodes took the honours and made no mistake, stepping up to cooly slot home with Kirkland diving in the opposite way.
Rovers looked in control but a goal out of nothing saw the home side level on 20 minutes. Lee Williamson was tardy in possession close to his own area to allow the fleet-footed Jermaine Johnson to race into the box to score low past Sandomierski.
The home side almost made it 2-1 on 24 minutes when Grzegorz Sandomierski saved well to deny Jeremy Helan at the near post. The resulting corner kick also caused consternation until Scott Dann hacked the ball away.
Ten minutes before the break the Owls were then handed a spot-kick of their own. Reda Johnson's deep cross into the Rovers box was claimed high and well by Sandomierski, but the official on the near touchline saw a push somewhere between Josh Morris and Grant Hanley on Leroy Lita and a penalty was awarded. It was very harsh.
Lita stepped up and like Rhodes made no mistake, Rovers' Polish goalkeeper diving in the oppostite direction as the ball flew into the top corner.
Rovers pressed for a way back into the game but were restricted to shots from distance, but efforts from David Dunn and Todd Kane were easily dealt with by Kirkland. At the other hand Rovers were thankful for Sandomierski once more as he saved well to thwart Lita.
After such a strong start to the game it was so disappointing with the way Rovers ended the half.
Rovers started the second half with renewed enthusiasm creating a host of chances in the opening exchanges after the restart. Neat passing between David Dunn and David Jones saw the ball worked to Jordan Rhodes but his snapshot was wide of goal.
Dunn and Jones would both fire over before Grant Hanley was denied by Kirkland from a Rovers free-kick.
Play continiued to be very much towards the Wednesday box as Rovers looked for an equaliser, a David Dunn free-kick was flicked on by Rhodes but again it was wide of goal. Then the Rovers top scorer was denied by Kirkland once more after chesting Dunn's pass down towards goal.
19 mintues from time Rovers finally grabbed the goal their second half display deserved. After David Jones' initial corner had been cleared out to the far side, subsitute Josh King swung the ball back in to the back post to where Scott Dann headed back across goal and into the back of the net.
It was nothing more than Rovers deserved and you very much felt that with the momentum that the visitors would go on and win the game, but they didn't account for the lighting pace of Jermaine Johnson.
On 78 minutes a Rovers attack broke down and Johnson took full advantage, racing towards the area before unleashing an unstoppable 25-yard strike that flew into the corner of the goal beyond Sandomierski.
Rovers pressed forward looking for a way back but a clear sight of goal was never found. Instead it was the home side who threatened the more, Jeremy Helan firing over when clean through, then with the last attack of the game Kieran Lee saw his shot saved by the legs of Sandomirski.
The result was harsh on Rovers after starting bright and then getting themselves back into the match only to lose it late on once more.
SHEFF WED: Kirkland, Buxton, Llera, Gardner (c), R. Johnson, Holden (sub Lee 59 mins), Coke, Olofinjana, Helan, J. Johnson (sub Maguire 85 mins), Lita (sub Howard 70 mins).
Subs not used: Bywater, Taylor, McCabe, Prutton.
Goals: J. Johnson 20, 78 mins, Lita (pen) 35 mins.
Booked: Kirkland, Olofinjana, Gardner, Reda Johnson.
ROVERS: Sandomierski, Kane, Dann (c), Hanley, Morris, Stewart (sub Kazim-Richards 56 mins), Williamson (sub King 63 mins), Lowe, Jones, Dunn, Rhodes.
Subs not used: Usai (GK), Givet, Pedersen, Nuno Gomes, Karim Rekik.
Goals: Rhodes 12 (pen) mins, Dann 71 mins.
Booked: Dunn, Williamson, Kane, Morris.