The Owls Under-23s slipped to a 2-0 defeat against Birmingham at Middlewood Road on Monday.
A young Wednesday side took to the field looking to build on recent back to back wins over Sheffield United and Leeds.
But after seeing chances go begging from Joe West and Conor Grant in the early throes of the game, the visitors went ahead just past the half hour mark.
Olly McCoy delivered a dangerous ball into the box from the right for George Baker to finish from close range.
Neil Thompson’s side began brightly after the break but were hit with a sucker punch after 59 minutes.
McCoy rose high in the box and glanced home from Odin Bailey’s free kick to double the visitors’ lead.
From that point onwards, Wednesday were restricted to half chances, with Preslav Borukov stopped in his tracks at the last by Geraldo Bajrami and substitute Omar Damba unable to turn home Alex Hunt’s centre in the final minutes.
Wednesday head to Charlton on Friday (2.00pm) in the Professional Development League.
Owls: Render, O’Grady (Waldock 69), West (Clarke 84), Hunt, Nielson, Lee, Hughes, Kirby, Borukov, Grant, Preston (Damba 60)