David Lee's men started the game on a positive note, only to be hit against the run of play by a high Jack Stobbs cross somehow fell beyond Jake Turner into the goal after four minutes of play.
Wanderers pressed forward still, with striker Connor Hall threatening on numerous occasions with his powerful pace and play.
The Whites equalised soon after, with a set piece resulting in Wanderers equalising as Erhun Oztumer volleyed home from the edge of the penalty area to score a fantastic goal.
Following this, another set piece resulted with trialist Chris David finding the head of defender Yoan Zouma, who nodded home from eight yards out.
The U23s kept on the front foot until the interval, but were unable to extend their lead before the break.
The Owls came out with a vengance in the second period and pulled one back through Conor Grant, who followed up a Liam Shaw effort to smash the ball into the top corner.
Mark Little constantly got in behind the defensive line on numerous occasions, with a curling cross into the area finding Connor Hall who volleyed at goal but Cameron McCulloch saved well in the Wednesday goal.
With a minute a regular time left on the clock, Oztumer was brought down on the edge of the home side's box in a dangerous position.
Trialist Christofer David stepped up and produced a superb curling effort that flew into the back of the net to seal all three points for the Whites.
This sees the U23s move up to third in the Professional Development League North Section, four points off league leaders Leeds United.
Wanderers XI: Turner, Little, Johnson, Zouma, Hartshorne, Jones-Griffiths, Brockbank, Earing (Broughton 70), David, Oztumer, Hall.
Unused substitutions: Navarro, Aspinall, Darcy, White.