Lee Barnard converted a second-half penalty to ensure an 11th win in 14 matches to continue the Shrimpers' stunning run.
Southend are now three points behind Scunthorpe, although they have played two games more than the Iron - who were not in action as they take on Luton Town in the Johnstone's Paint Trophy final on Sunday.
Southend close gap to play-offs
Leicester City remain top, although their lead has been cut to two points after they were held to a 2-2 draw by Carlisle United at the Walkers Stadium.
Michael Bridges gave the visitors a surprise lead, but Matt Oakley levelled for the home side after a series of fine saves by the Carlisle keeper Ben Williams.
Leicester dominated and took a deserved lead through Matty Fryatt with two minutes to go, although Scott Dobie grabbed a late leveller for the Cumbrians.
Peterborough United took advantage of Leicester's slip with a 2-1 win at Oldham Athletic.
Craig Mackail-Smith scored both for Posh, with Chris Taylor netting for the Latics.
Goals from Gary Alexander either side of the break inspired Millwall to an important 3-1 win over Walsall to keep the automatic promotion dream alive in south London.
MK Dons recorded a 2-0 home win over Brighton. Ali Gerba and Jason Puncheon scored for the Dons, who remain adrift of the automatic promotion places.
Leeds United chalked up a 1-0 victory at Colchester - they have now won seven of their last nine games - thanks to a 29th minute strike from Luciano Becchio.
Dean Morgan's goal after 25 minutes gave Leyton Orient a 1-0 win at Cheltenham Town.
Hartlepool United grabbed a 4-2 home win over Hereford United that eases their relegation worries, but the Bulls look destined for League Two football next season.
Swindon Town and Crewe Alexandra played out a goalless draw at the County Ground, as did Stockport County and Yeovil Town at Edgeley Park.