Brian Laws welcomed his old employers to Hillsborough but the Iron showed scant regard and stole away with all three points. Martin Paterson's first half brace did the damage, overturning Deon Burton's opener as Wednesday went down once more on home soil.
The Owls made two changes from the side that won at Stoke on Saturday. Long term injury victim Francis Jeffers gave way to Burton, while ex Iron utility man Richard Hinds came in at right back in place of Lee Bullen, who dropped to the bench.
Wednesday were first to pose a threat after a cagey opening; Burton O'Brien skewing wide following a neat link-up with Burton. The hosts went closer on ten minutes when in-form striker Marcus Tudgay capitalised on more good work from Burton and fired a snapshot that flew narrowly past the post.
Neither side took a true grip on the game, with much of the play unfolding in a congested midfield. SWFC were enjoying the lion's share of possession but the cutting edge evident against Stoke was notable by its absence.
But the game exploded into life in the 23rd minute. Glenn Whelan burst into the box from the engine room only to be felled by Jim Goodwin and Burton stepped up to comfortably dispatch the Owls' first spot-kick of the season.
The Iron's response was instant. Goodwin launched a free kick into the danger area, Andy Butler headed across goal and Paterson drove home to haul the visitors level. Paterson then almost doubled his account with a blistering drive that Lee Grant was relieved to see fly into the Kop.
The Owls suffered another blow 34 minutes in when captain for the night Richard Wood fell awkwardly and was stretchered from the field in some distress with a dislocated shoulder. Bullen slotted into the SWFC defence as a result.
Wednesday's first half misery was complete six minutes before the interval when Scunthorpe stole into the lead. Cleveland Taylor broke down the right flank and hit a low, pacey cross for the on-rushing Paterson, who drilled in at the back post to put SUFC in the ascendancy.
The same player headed just over the bar from a corner right on half time and it was Wednesday that welcomed the interval.
Akpo Sodje replaced Burton at the start of the second half and the substitute's aerial threat almost played Tudgay in just after the resumption. Wednesday then forced three corners in as many minutes, the second of which saw Scunthorpe survive a strong penalty shout when a stray hand appeared to deflect O'Brien's flag kick.
The Owls were certainly showing an appetite for a revival and launched a string of attacks with the Iron seemingly content to sit on their lead. Jermaine Johnson foxed two defenders and went headlong into the box but blasted his shot high and wide.
With Hillsborough finding its voice, Bullen thumped a shot goalwards after Tudgay flicked down Graham Kavanagh's cross but the linesman flagged for offside to avert the threat for Scunthorpe.
With 20 minutes to go, the Iron almost scored with their first attack of the second period. Kevan Hurst swung over a teasing corner and Butler headed towards goal but Tudgay came to the Owls' rescue on the line.
Wednesday showed plenty of willing as the clock ran down - Kavanagh and Whelan both warmed the hands of Joe Murphy from distance - but Scunthorpe held on to emerge triumphant.
SWFC: Grant; Hinds, Johnson, Wood (c) (Bullen 35), Spurr; Johnson, Kavanagh, Whelan, O'Brien (Esajas 76) Burton (Sodje 45), Tudgay
Subs not used: Burch, Lunt
Booked: Burton
Scunthorpe: Murphy, Crosby (c), Butler, Byrne; Youga, Taylor, Hurst, Goodwin, Sparrow (Williams 81), Hayes (Forte 71), Paterson (May 84)
Subs not used: Lillis, Iriekpen
Booked: Butler, Youga, Crosby
Attendance: 21,557
Referee: A. Taylor
