A first half double from Chris O'Grady and a fine solo strike after the break from Jermaine Johnson gave the Owls a deserved win at Glanford Park on Tuesday.
O'Grady, who was superb throughout, struck&nbsp;inside the opening&nbsp;60 seconds&nbsp;before doubling his own tally after 18 minutes with a fine header from Chris Lines' corner.
Johnson then wrapped up the points a minute after the break after bursting through into the area to finish confidently past Iron keeper Sam Slocombe.
Jordan Robertson netted a consolation for the hosts on 55 minutes as the&nbsp;Owls posted three vital points and move into joint second in League 1.
Gary Megson made five changes from the 2-2 draw against Hartlepool on Saturday, with Stephen Bywater, Daniel Jones, Miguel Llera, Johnson and Liam Palmer all in the starting line-up.
And the visitors made a dream start under the floodlights at Glanford Park, with O'Grady scoring after 47 seconds.
It was Llera who played an inch-perfect ball over the top of the Iron defence and O'Grady did the rest with an assured touch under pressure, before calmly slotting past&nbsp;Slocombe.
Scunthorpe almost equalised with a header from Andy Barcham that flew just over the bar before O'Grady doubled his tally on 18 minutes.
Gary Madine did well to win a corner down the left and, from the resulting flag kick, Chris Lines picked out the imposing figure of O'Grady who headed home from six yards.
Stunned by the Owls' early dominance, Scunthorpe went in search of a goal to halve the arrears but struggled to test the recalled Bywater.
Wednesday continued to look the more threatening in front of goal as the Iron failed to clear a flurry of corners, with the ball eventually dropping to Palmer who dragged his effort wide of the target.
It was another corner that saw O'Grady come within inches of registering his hat trick.
Another dangerous delivery from Lines fell to O'Grady who, with his back to goal, improvised with a smart overhead volley that bobbled off the outside of the post and behind for a goalkick.
Two minutes before the break, O'Grady once again called Slocombe into action with a strike from the left channel that the&nbsp;keeper managed to parry away from danger.
As the action resumed in the second period, so did the Owls attacking threat as Jermaine Johnson fired Wednesday into a 3-0 lead on 47 minutes.
The Jamaican latched onto a loose ball in Scunthorpe territory and raced past his marker before side footing home in front of the jubilant Owls fans behind the goal.
But just as the contest appeared to be slipping away from the hosts, Robertson gave the Iron a lifeline, stooping low to head past Bywater from Josh Walker's corner.
It was end to end action at Glanford Park as O'Grady went close to his treble once again - and would have done so - but for a fine diving save from Slocombe.
Johnson was seemingly unstoppable throughout the second half with the Iron defence struggling to halt the Jamaican's pacey runs upfield.
O'Grady was giving the home side a similar headache - with the only thing lacking from his game on the night being a hat trick that he had so richly deserved.
Scunthorpe: Slocombe, Nolan, Togwell, O'Connor (Grant 53), Robertson, Thompson, Walker, Reid, Canavan, Barcham (Duffy 53), Ribeiro (Wright 4)
Unused substitutes: Lillis, Mozika
Wednesday: Bywater, Otsemobor, Batth, Llera, D Jones (Beevers 38), J Johnson (M Jones 90), Lines, Semedo, Palmer, O'Grady, Madine (Morrison 89)
Unused substitutes: Weaver,&nbsp;Lowe