Phil Brown's side slumped to their fourth successive defeat, despite dominating the majority of the first half at Roots Hall.
Southend pushed forward in search of the game's opener, but found Scunthorpe goalkeeper Sam Slocombe in fine form as he kept headers from Ryan Leonard and then Freddy Eastwood out.
However, their good work counted for nothing as Ben Coker's attempted header only played Iwelumo in on goal and he kept cool to nod home the game's only goal.
The hosts struggled to get back into the game, former Scunthorpe winger Kevan Hurst went closest with a drive from distance, but Slocombe again saved well.
At the other end, Southend keeper Dan Bentley had to be alert to keep the scoreline down, keeping Sean McAlister's crashing effort out, while also seeing Eddie Nolan's header drift wide.
Scunthorpe, who have lost just one of their seven league games so far this term, move up to seventh ahead of the weekend's action.
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