The Owls were knocked out of the Emirates FA Cup after a 3-2 to defeat to Shrewsbury Town at Greenhous Meadow.
Lewis McGugan opened the scoring inside 20 minutes for the visitors after his long range free kick flew past everyone in the box before outfoxing goalkeeper Jayson Leutwiler at his back post.
The Shrews equalised eleven minutes into the second half after Jean-Louis Akpa Akpro nodded home from Andy Mangan’s deep cross.
Wednesday regained the lead with 14 minutes left on the clock, when McGugan grabbed his second of the afternoon with a sweetly struck shot from distance.
With three minutes remaining of normal time the home side were awarded a penalty which was superbly saved by Lewis Price, but Shaun Whalley was on hand to dispatch the rebound.
And deep into stoppage time the League One side scored the winner through defender Jack Grimmer who slammed home a header from less than six yards out.
Owls boss Carlos Carvalhal made nine changes to his starting XI for the trip to Shropshire.
Vincent Sasso and Gary Hooper were the two players in the line-up who started last weekend’s 1-1 draw at Reading, with midfield duo McGugan and Marco Matias both involved after long injury lay-offs.
There was also a debut for Joe Bennett on the left hand side of the defence, his first appearance since joining on loan from Aston Villa.
Wednesday started the tie on the front foot as midfielder McGugan lashed over from 20 yards out inside six minutes.
The blustery conditions were always going to be a difficult master at the Greenhous Meadow, but on 19 minutes the Owls broke the deadlock.
Matias was brought down around ten yards outside of the penalty area, with the lively McGugan’s direct free-kick whizzing past those in the box before squeezing inside Leutwiler’s far post.
With the hosts struggling to make their mark on the match, McGugan was again involved as he whipped another ball in from the left that deflected off Hooper’s knee before looping just over.
The visitors were afforded two more chances before the break to add to their lead.
First was Matias who had his powerful effort parried to safety by Leutwiler, before striker Lucas Joao headed over from a dangerous Sougou cross.
The hosts emerged from the dressing room a rejuvenated side as they immediately threatened through Larnell Cole, but his shot went straight at keeper Price.
On 56 minutes Shrewsbury drew level with only their second shot of the match.
Mangan escaped his defender down the right hand side before crossing to the back post for Akpa Akpro to nod home from close range.
Level in the match, the Owls came close to retaking their lead as Jose Semedo darted through the middle of the park before forcing Leutwiler into a diving save.
At the other end Akpa Akpro dodged the offside trap before bearing down on goal, but Price produced a smart stop to deny the Shrews goalscorer from doubling his tally.
With the tension building heading towards the final period of the match, step forward McGugan to fire Wednesday back into the lead on 76 minutes.
After receiving the ball from 25 yards out, the midfielder couldn’t have hit it any sweeter as his shot flew off his boot before swerving inside the goalkeeper’s right hand post.
However the League One side managed to hit back in the dying minutes of the game after Akpa Akpro was brought down by Vincent Sasso for a penalty.
Price pulled off a sensational save to his right to keep out Akpa Akpro’s spot kick, but could do nothing about the rebound which Whalley tucked home.
With six minutes of stoppage time added on, Shrewsbury struck on 97 minutes through young defender Grimmer, who turned home from close range to send the Shropshire side into the fifth round of the cup.
Wednesday: Price, Palmer, Turner, Sasso, Bennett, Sougou (Wallace, 70), Semedo, McGugan, Matias (Lee, 78), Hooper (Nuhiu, 61), Joao.