French winger Helan, who moved to Hillsborough from Manchester City on Thursday, poked home the winner in the 41st minute at Glanford Park on Saturday, after Matt Sparrow had spurned two decent chances for the Iron.
Helan, who made 25 appearances for Wednesday during a loan spell last season, also brought a fine save from home goalkeeper Sam Slocombe early in the second half, while Owls midfielder Rhys McCabe saw a fierce drive crash back off the angle of post and crossbar.
Matt Godden should have levelled for United late on in the pre-season friendly, but he fired wide with the goal gaping.
Owls manager Dave Jones was pleased with his side's workout in the heat at Glanford Park.
He told the club's official website: "It was sweltering out there today but it can only do the players good.
"This stage of pre-season is all about the fitness and although it is nice to win any game, what we are looking for now is the lads moving in the right direction.
"That was a good test for us and we have come through it okay. Scunthorpe played some nice football but I thought we were good value for the win."