The Owls initially went behind just before the break but goals from debutant Sam Walker and Daniel Trott sealed three important points as their title hopes stay alive.
Marcus Newell made just one change from Saturday's 0-0 draw with Tadcaster Albion. Laurence McKay replaced Lawrence Heward who was unavailable.
The Owls started brightly with Luke Mascall volleying narrowly wide after five minutes from some lovely build-up play.
Then Athersley had a spell of possession which had the Owls back line worried. Keeper Liam Higton and defender Peter Winn got in a mix-up which allowed Martyn Scully to have a shot but he squandered the chance to give Athersley the lead.
At the other end Trott went close but found Neal May in fine form denying the striker with a great one-handed save.
Just before the break Athersley took the lead. Danny Cawley found the back of the net as he headed home a fine cross from the right.
With no changes at the break the Owls went on an immediate search for an equaliser but former Grimsby Town midfielder Caine Winfarrah could only see his goal bound shot deflected wide in the opening minutes of the half.
Mascall, looking for his 10th of the season hit the side netting from a tight angle with 18 minutes to go.
Newell then made a bold move bringing on debutant Walker for his first senior appearance. It made an immediate impact as he had the back in the ball of the net within eight minute of coming on. He beat the offside trap then shot under Neal to level the game.
Just five minutes later and the Owls were in the lead. Trott half-volleyed the ball into the net from close range to send the travelling army of support into ecstasy and to send the Owls home with all three points.
The win sees the Owls level on points with Tadcaster Albion, however they do have three games in hand but as this season proves, anything can happen!