A late leveller by Sam Baldock rescued a point for Bristol City at Ashton Gate.
The Owls led through a first half Jermaine Johnson strike but in second half stoppage time, Baldock volleyed home to earn his side a point.
It was a cruel blow for Wednesday who had held firm up to that point and were seemingly heading towards a vital victory.
Manager Dave Jones made five changes from the side that triumphed 2-1 over Barnsley on Saturday.
Striker Steve Howard made his debut for the club following his loan move from Hartlepool, while David Prutton and Giles Coke returned in central midfield.
Kieran Lee stepped in at right back for the suspended Lewis Buxton.
Wednesday were looking to build on that vital win over the Tykes while three points for City was a must if they were to keep alive any hope of avoiding the drop.
The Robins made a bright start and created the first clear opening on six minutes.
Baldock centred for Stephen Davies, who looked odds on to bury his header into the net but for a vital interception from Miguel Llera.
The early pressure was coming from the hosts and Chris Kirkland was called into action twice within the space of two minutes.
The Owls goalkeeper was at full stretch to push the ball to safety following a curled effort from Lewin Nyatanga before denying Davies’ low drive with his feet from close range.
Jermaine Johnson did well to fashion a chance on 20 minutes after racing past a cluster of defenders but fired over the bar before City promptly responded at the other end.
Midfielder Liam Kelly sent in a powerful cross that needed just a touch from Davies to divert goalwards but there was a fraction too much pace on the ball for the striker to capitalise.
The warning signs were there for Wednesday as Brendon Moloney delivered dangerously into the box but Marvin Elliott could not adjust in time to finish at the back post.
But despite the Robins’ pressure, the home side were dealt a huge blow on 35 minutes when Wednesday hit the front through Jermaine Johnson.
Debut man Howard won possession and sent the pace ace through one-on-one with Tom Heaton, and the Jamaican kept his composure to apply a neat finish after rounding the keeper.
Back came Bristol City, though, who had a golden chance to restore parity moments before the break.
Baldock slid the ball towards to the unmarked Davies, who was just yards from goal, but the striker couldn’t connect and the chance had gone.
City started the second half as they did the first and the Owls were on the back foot – but it was Jones’ men who almost bagged a second on the counter.
Jermaine Johnson weaved his way past three challenges and drove hard and low across goal, with the onrushing Howard a whisker away at the far post.
That proved the Jamaican’s last involvement as injury dictated his withdrawal and JJ’s replacement, Leroy Lita, smashed into the side netting with his first touch after breaking free down the left of the penalty area.
With 15 minutes left on the clock, there was drama as Greg Cunningham went down in the area under a challenge from Kieran Lee – the referee immediately stopped play but cautioned Cunningham for simulation.
Nyatanga was thwarted by a superb challenge by Anthony Gardner in stoppage time but City were not to be denied.
Deep into added time, Kirkland was challenged in the air by Elliott and the ball dropped down to Baldock who smashed home on the half volley to level late in the contest.
Bristol City: Heaton, Fontaine, Nyatanga, Baldock, Kelly (Kilkenny 68), Skuse (Anderson 84), Pearson (Adomah 68), Davies, Cunningham, Moloney, Elliott
Unused substitutes: Gerken, Carey, Howard, Bates
Owls: Kirkland, Lee, Llera, Gardner, R Johnson, Pugh, Prutton, Coke (Semedo 77), Helan, J Johnson (Lita 52), Howard (Madine 65)
Unused substitutes: Bywater, Mattock, Taylor, Maguire