Paddy Madden got the winner for the home side, who looked comfortable throughout the afternoon.
The Iron went into the game unchanged from the previous victory over Coventry City. Luke Daniels was the man between the sticks, and in front of him remained the back four of Scott Wiseman, Murray Wallace, David Mirfin and Conor Townsend.
Jamie Ness, Stephen Dawson and Neal Bishop were once again the midfield three, and Madden, Tom Hopper and Luke Williams continued as a front three.
United had the better of the opening stages, and ten minutes in, Dawson forced Shrimpers 'keeper Daniel Bentley into a fine save. The captain turned neatly on the edge of the box, before unleashing a left footed drive, which Bentley did well to tip round the post.
From the resulting corner though, the Iron got themselves ahead. Williams played a one-two with Ness, and then whipped the ball into the area. His cross evaded everyone, except from Madden, who headed home from close range, after finding some space at the far post.
The lead was soon nearly doubled as Bishop hooked a volley goalwards. However, he couldn't repeat Madden's feat, as Bentley came out and smothered his effort.
It was clear to see which side were in the ascendancy, as the Iron continued to cut the visitors' defence open at will. Just before the half an hour mark a fluid passage of play between Hopper, Williams and Bishop almost resulted in a second, but as Williams tried to feed the ball to Bishop, Bentley superbly foiled the midfielder.
Despite their first half dominance, the hosts couldn’t find a second before the interval, and they went in with just a one goal advantage.
Much like in the first period, the Iron started brightly from the kick off, with Williams cutting in from the left hand touchline, before striking a deflected effort over the crossbar. Mirfin then sent a header towards the far corner of the goal, which drifted inches wide of Bentley's post.
Full-back Wiseman was keen to get in on the act too, and he went close to adding a second when he drove into the penalty area. However his shot was blocked before it reached an unmarked Hopper.
15 minutes into the half, visiting goalkeeper Bentley almost had a moment to forget, when he came for a cross and didn't gather. The ball then fell to Madden, but with Bentley stranded, the Irishman could only stab wide under pressure.
United were banging repeatedly at the Southend door, but it wouldn't open. Wallace was the next to go close, with a thumping header off the crossbar. The Scot had Bentley beaten all ends up, but like on so many occasions throughout the afternoon, the Iron didn't get the reward they deserved.
Phil Brown's side did go close to finding a route back into the game, when substitute Noel Hunt sent a dipping free kick towards the right corner of Daniels' goal. But the United stopper preserved the lead, with a fine diving save.
As the fourth official raised the board to indicate an additional seven minutes of added time, the visitors poured forward, and would have probably equalised if not for a courageous last ditch block from Mirfin.
The warning from Brown's side spurred the Iron into pressing for the killer second goal. Substitute Gary McSheffrey nearly got it when he broke into the box, but his fizzing strike was palmed away by Bentley.
McSheffrey's effort would be the last of the game, as despite the hefty amount of added time, United held out for another vital three points.
Scunthorpe United: Daniels, Wiseman (Clarke, 86), Mirfin, Wallace, Townsend (Laird, 86), Bishop, Dawson, Ness, Williams (McSheffrey, 86), Madden, Hopper.
Substitutes not used: Anyon, King, Vose, Luer.
Southend United: Bentley, Thompson, Payne, Atkinson, Bolger, Barnett, McQueen (Wordsworth 50), O'Neill, Kamara (Loza 50), Barrett (Hunt 59), Hendrie.
Substitutes not used: Smith, Coker, McLaughlin, Deegan.