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Iron skipper Andy Crosby and Richard Hinds gave dominating displays, and needed to as the Shrimpers took charge of the second half, just the opposite to the opening spell.
Luke Guttridge was a key figure for the visitors and with Shaun Goater and Wayne Gray always a threat they looked a strong combination.
With a new-look attack in teenagers Billy Sharp and Andy Keogh, Scunthorpe began in lively fashion.
It was the veteran midfielder Peter Beagrie who combined well initially with Sharp on the left and as the ball was crossed to Keogh, his effort struck keeper Darryl Flahavan's legs and was cleared by Che Wilson.
Richie Ryan and Keogh were then involved in a smart move before setting up Beagrie, whose 13th minute shot rattled the woodwork.
Southend were themselves trying the keep moving forward and two minutes later Goater created an opening for Mark Gower, who flashed a shot wide.
On the half hour mark, Flahaven had to be alert to punch away a Sharp header from Beagrie's left-wing cross.
Scunthorpe's incisive football brought them reward in the 36th minute when Matt Sparrow played the ball into the box from the right, Sharp allowed it to run through and Ian Baraclough tucked away in fine style.
Southend should have equalised just before the interval whistle. Crosby lost out in a challenge with Guttridge, and Gower clipped the ball into the box for Goater, whose control let him down.
Scunthorpe had a let-off in the opening minute of the second half when Marcus Williams and Ryan failed to connect with each other, allowing the Shrimpers to break, but they were unable to take advantage.
As the game flowed from end to end Beagrie and Keogh both saw efforts fly inches wide, before Paul Musselwhite clawed away a header from Andy Edwards and then blocked a shot from Goater.
In the closing stages Guttridge was again very close and Musselwhite had to dash out of his area to prevent substitute Mitchell Cole from scoring.