The Owls Under-23s went down 2-1 against Bolton on Monday evening.
Two first half goals from Luca Navarro were enough to earn the points for his side at the Lancashire FA County Ground.
Jack Stobbs issued a late reply for Neil Thompson’s men but it proved nothing more than a consolation as Wednesday fell to back to back defeats.
The game provided more minutes for defender Joost van Aken, who played just over an hour of the PDL2 clash.
The Owls made a promising start with Stobbs in a lively mood and drawing two early saves from Bolton goalkeeper James Aspinall.
The breakthrough, though, came in the 31st minute when Navarro sent a blistering strike past Cameron McCulloch from just outside the area.
Wednesday then had to withstand pressure from the hosts as Joe Pritchard forced two excellent stops from McCulloch and then right on the stroke of half time, Bolton found a way through to double their lead.
Pritchard went down in the box, the referee pointed to the spot and Navarro converted from 12 yards to give the hosts a cushion going into the break.
Wednesday battled after the break and went close through Preslav Borukov and Ciaran Brennan in a frustrating half for the visitors.
But the Owls' persistence earned a consolation goal three minutes from time when Stobbs’ cross-cum-shot flew past Aspinall and into the net to set up a tense final few moments.
Wednesday return to action on Friday 16 November against Barnsley at Hillsborough (7.00pm).
McCulloch, Hughes, West, J Lee, Brennan, van Aken (Rice 64), Lonchar, Kirby, Stobbs, Hunt (Grant 46), Clarke (Borukov 46)