The League One final is the first play-off this weekend to not see any goals in normal time, but was the first not to go all the way to penalties as the Owls won it at the death in extra time thanks to Josh Windass' bullet header.
Barnsley had a penalty shout waved away by VAR when Liam Kitching went down in the box in the second half of normal time with neither team drawing first blood yet.
It then got worse for the Tykes, as they were reduced to ten men following Adam Phillips' straight red card for his challenge on Owls forward Lee Gregory.
But Barnsley battled on, taking Wednesday to extra time with the score still at 0-0.
The Owls had an effort cleared off the line just after the restart, before Barry Bannan just missed the target, firing his effort over the bar.
MORE IN EFL
Stelling fumes at VAR as Barnsley man is sent off in League One play-off final
Laura Woods destroys Twitter troll with savage response after Sheffield Wednesday comeback
Barnsley goalkeeper Harry Isted then made a phenomenal finger tip save to deny their rivals once again just minutes later, before the Tykes missed a golden opportunity to score on the counter, with Luca Connell firing wide.
Wednesday then thought they'd found the winner as Will Vaulks' long-distance rocket hit the back of the net only to be ruled out for offside.
But the Tykes ran out of steam and couldn't take the tie against their South Yorkshire rivals to a shootout, as Windass - son of Dean Windass, who scored a famous goal play-off goal for Hull City in the Championship play-off final 15 years ago - fired Wednesday back into the second tier in the three minutes into stoppage time of extra-time.
Bannan - who had just been subtiututed off - was seen running to hug and kiss Dean after the goal went in as the pair celebrated promotion.
Most read in EFL
Stelling fumes at VAR as Barnsley man is sent off in League One play-off final
Barnsley vs Sheffield Wednesday LIVE: Owls and Tykes clash for final Championship place
Tom Lockyer posts update from hospital after Luton captain collapsed during play-off final
Inside Luton's promotion party as stars plot week of celebrations before Las Vegas trip
Darren Moore's side will return to the Championship at the second time of asking after missing out in the play-offs last season.
Tottenham 
Newcastle 
Atalanta 
Bayer Leverkusen 
Cagliari 
Fiorentina 
Baltika 
Lokomotiv Moscow 
CSKA Moscow 
Ural 
Orenburg 
Spartak Moscow 
Manchester Utd 
Manchester City 
Celtic 
Rangers 
Polissya Zhytomyr 
Shakhtar Donetsk 
Rukh Lviv 
Dynamo Kyiv 
FC Kaiserslautern 
Lyon 
Paris Saint Germain 
Real Madrid 
Betis 
Real Sociedad 
Atletico Madrid 
Celta Vigo 
Valencia 
Empoli 
Roma 
Frosinone 
Udinese 
Lazio 
Sassuolo 
Napoli 
Lecce 
Verona 
Inter 
FC Porto 
Sporting CP 
Amorebieta 
Espanyol 
Sevilla 
Barcelona 
Olympiacos Piraeus 
AC Milan 
Borussia Dortmund 
Cartagena