A brace from Franck Betra helped the ten-man Owls youngsters bounce back from going a goal down to beat their Swansea counterparts and continue their strong start to the season at Hillsborough.
Rafa Floro was sent off for a deliberate handball on the line just before the break with Kenji Gorre putting the Swans ahead from the spot.
But Wednesday refused to lie down and battled well after the break with the lively Betra equalising from the spot after being fouled himself before rifling home a brilliant individual effort to claim all three points.
The clash also saw the return to action of injury victim Lewis Buxton, who was given an hour of game time. And new signing Claude Dielna played the entire 90 minutes in a variety of positions.
Dielna partnered Buxton at centre back during the first half before sitting on the left of defence with the Owls down to ten men and switching between three and four players at the back.
And the Frenchman finished the game as part of a three man midfield, showing good strength and an assuredness on the ball.
Confidence in possession oozed from Betra as he grabbed the winning goal six minutes from time.
Picking up possession 30 yards from goal, Betra set off on a surging diagonal run, holding off several challenges before clipping the ball past David Cornell from ten yards.
The forward’s winner was just what the Owls deserved after maintaining their effort levels throughout against the Premier League outfit’s development side.
It all seemed to be going in the Swans’ favour at half time.
Floro got in the way of a Jay Fulton header on the line with the referee initially signalling for a corner until his assistant flagged for handball.
The Portuguese full back was sent off with Swansea awarded a penalty which Gorre slammed low to put his side ahead.
The South Wales side looked set to see the game out in comfortable fashion as they kept possession patiently early in the second half.
But they were punished for failing to maintain their work rate by a determined Wednesday side.
The deserved equaliser came ten minutes from time when Betra was held back in the box by Fulton before putting his spot kick into the top corner.
And four minutes later came his superb winner which gave Lee Bullen’s men their second win from four matches.
Wednesday U21: Wildsmith, Young, Buxton (Sanders), Dielna, Floro, Meadows, McCabe, Croasdale, Grozdinov (Havilland), Betra, Dieseruvwe (Tracey). Not used: McDonagh, Duffy.
Swansea U21: Cornell, Shephard, Tancock, Gallifuoco, Kingsley, Fulton, Barrow, Jones (Loveridge), King, Gorre, Samuel (March). Not used: Davies, Roberts, Hanley.