A last minute penalty converted by Blackpool striker Kevin Phillips ensured the FA Cup fourth round clash finished 1-1 at Bloomfield Road.
Clinton Morrison had given the Owls the lead six minutes after the restart but the late strike means the tie will now go to a replay at Hillsborough.
The home side made a strong start to the cup clash as left back Bob Harris fired an early warning shot just wide of Stephen Bywater's left hand post.
Blackpool were seeing most of the ball in the opening ten minutes and it was another Harris drive that came close to breaking the deadlock.
Danny Batth did well to intercept Matt Phillips' cross from the right but the defender's clearance fell straight to the lurking Harris who volleyed just over the angle.
The Owls then hit back with swift attack of their own as Clinton Morrison saw his attempt finish agonisingly wide of the target.
Ryan Lowe was brought a good stop at the near post from Matthew Gilks but Morrison's instinctive stab goalwards on the rebound flashed just wide of the target.
But Blackpool were looking dangerous on the counter and Stephen Bywater was called into action on 15 minutes.
Neal Eardley broke quickly down the right and centred for Keith Southern, who's firm header was pushed to safety by the Wednesday keeper.
It was Gilks' turn to come to his side's rescue moments later, saving impressively from Lowe's crisp volley from inside the six yard box which seemed destined for the top corner.
Gilks then spared Southern's blushes five minutes before the break.
The Blackpool skipper's back pass back fell short to Lowe, but the striker couldn't get the necessary elevation on his lob to beat the outrushing Tangerine goalkeeper.
Bywater ensured the scores stayed level at the break, as the Owls keeper made a fine stop from Billy Clarke's first-time drive across goal.
It took just six minutes after the restart before the Owls edged in front in the FA Cup tie through Morrison.
As David Prutton sent Lowe scampering in on goal, Gilks was able to come and clear, but only as far as Morrison who applied an expert looped finish into the far corner.
The goal had given the Owls a visible boost while the hosts struggled to find any way through a resolute Wednesday defence.
The late pressure was coming from the Seasiders who were desperately seeking a way back into tie.
Dangerman Kevin Phillips had a sight of goal ten minutes from time but put his half volley wide of Bywater's goal.
After good wing play down the left from Chris Sedgwick, the midfielder found Chris O'Grady inside the 18-yard box who tested Gilks with a low drive, with the Blackpool keeper gathering at the second attempt.
But the Tangerines drew level from the spot in the 90th minute.
Sedgwick impeded Gary Taylor-Fletcher and Kevin Phillips did the rest from 12 yards to bring the tie back to S6.
Blackpool: Gilks, Southern (Taylor-Fletcher 52), Eardley, Clarke (Dicko 63), M Phillips, Basham, Cathcart, K Phillips, Angel (Ince 80), Harris, Wilson
Unused substitutes: Bruna, Baptiste, Halstead, Fleck
Wednesday: Bywater, Buxton, Batth, R Jones, Beevers, Prutton, Lines, Palmer (J Johnson 46), Sedgwick, Morrison (O'Grady 75), Lowe (Otsemobor 59)
Unused substitutes: Weaver, Semedo, Madine