But the Iron will be relieved that goalkeeper Paul Musselwhite pulled off a vital double save from Mark Bentley late on and referee Paul Taylor awarded the Shrimpers a free-kick and not a penalty when skipper Andy Crosby appeared to handle in the box.
Yet Brian Laws' men should have been home and dry long before then as they enjoyed better spells for the majority of the match.
And it was only fine goalkeeping from Darryl Flahavan in his 200th appearance for Southend that provided the visitors with those few nervy moments in the latter stages.
The hosts started the brighter of the two sides but Scunthorpe soon began to exert their influence with controlled passing amid some good build-up play.
But the Southend defence was up to the task to mop up any danger and the visitors had to wait until the 23rd minute before getting a shot away.
That came when Stevland Angus' long ball up the centre of the pitch was flicked on by Steve Torpey for fellow striker Jon Walters to shoot. Flahavan dived to block the effort and then pushed the loose ball clear.
Blues replied with Nicky Nicolau's 20-yarder being gathered low by Musselwhite in injury time, before Flahavan saved a Torpey effort.
Four minutes after the restart, Flahavan made a brilliant reaction save to deny Ian Barraclough.
Neither side made much further headway until Southend boss Steve Tilson made a double substitution after 67 minutes and the arrival of winger Mark Gower sparked the hosts into life.
Kevin Maher's long ball for Freddy Eastwood on 78 minutes was handled by Crosby but referee Taylor ignored the Southend striker's penalty appeals, much to the annoyance of home fans.
Then five minutes from time Eastwood dummied Che Wilson's centre, allowing Bentley to shoot only to see Musselwhite save his first attempt and the follow up, before Crosby cleared the loose ball.