Fleetwood ended Wednesday’s Emirates FA Cup hopes with a 1-0 win in this fourth round replay.
Carlos Mendes Gomes scored the only goal of the game, halting Owls’ long unbeaten run but leaving the visitors free to focus fully on the primary aim of promotion.
The contest could have gone either way, with good chances at both ends, and it was Mendes Gomes that took the one that mattered.
It was all change for the Owls, with only Liam Palmer in the starting line-up from the team that beat Plymouth in the league on Saturday.
Darren Moore handed a debut to academy starlet Sean Fusire, while fellow youngster Adam Alimi-Adetoro took his bow as a half time substitute.
Cod Army manager Scott Brown also shuffled his pack, fielding a much-changed starting XI to that of the first tie at Hillsborough, where goalscorer Promise Omochere was inches away from a dream start, nodding a Phoenix Patterson cross wide.
Omochere then went closer still, spinning in the box to find space and execute a fierce drive that smashed against the upright.
The Owls went downfield and this time the woodwork came to Fleetwood’s rescue as Lee Gregory’s header hit the underside of the crossbar following fine work down the left from Palmer.
The hosts responded with Patterson curling a clever shot from distance that had David Stockdale springing across his goal and the keeper was relieved to see the ball bend just off target.
The breakthrough came right on the hour and it was Patterson again the provider, sending an inviting cross into the danger zone that Mendes Gomes glanced into the roof of the net.
Wednesday, bolstered going forward by Josh Windass and George Byers from the bench, came on strong in search of an equaliser.
Fisayo Dele-Bashiru had claims for a penalty turned down after tangling with Brendan Wiredu and Byers was not far away with an outswinger that flew the wrong side of the post.
But with Fleetwood content to sit back and hold on to their lead, the Owls were left frustrated in the closing stages and the Lancashire outfit advance to round five.
Wednesday: Stockdale, Fusire (Windass 70), Hunt, Palmer (Iorfa 46), Famewo (Alimi-Adetoro 46), Brown, Adeniran (Byers 70), Bakinson, Dele-Bashiru, Gregory (Smith 46), Wilks