Wednesday, with three wins from their last five games, were in trouble with four minutes gone when on-loan defender Michael Johnson lost his footing under pressure from Paul Hayes, but before the ex-Barnsley striker could finish, Richard Wood moved in to clear.
Midfielder Burton O'Brien tried his luck from long range, shooting high and wide before Marcus Tudgay, the two-goal hero in Saturday's 4-2 win at Stoke, almost broke the deadlock, his snap shot curling inches wide of the target after Deon Burton's strike was blocked.
The Sheffield side snatched the lead on 23 minutes when Glenn Whelan's strong run into the area was brought to an abrupt halt by full-back Kelly Youga, Burton coolly sending keeper Joe Murphy the wrong way as he drilled the ball into the left-hand corner.
Scunthorpe, were back on level terms just a minute later, Wednesday falling victim to a textbook goal. Jim Goodwin floated the ball to the far post, Andy Butler headed back into the goalmouth and Paterson added the finishing touch, sidefooting past the helpless Lee Grant from close range.
Paterson grabbed his second in the 40th minute after slick Scunthorpe cut through Wednesday's paper-thin defence. Cleveland Taylor, in space on the right flank, squaring the ball to the striker as he charged into the box to finish crisply from ten yards.
Paterson almost completed a hat-trick in first-half injury time as he stretched to meet Kevan Hurst's corner heading inches over the target from six yards.
Wednesday pounded the Scunthorpe goal after the interval, but were caught on the break in the 71st minute, Hayes finishing with a fierce strike punched away by the diving Grant.
Jermaine Johnson weaved his way past two defenders but ballooned the ball high into the stand and Tudgay saw his stinging shot from 30 yards scooped up by Murphy as Wednesday battled for a late equaliser to no avail.