Duane Ofori-Acheampong's 31st-minute winner means that victory over Essex rivals Colchester United next Saturday in Blues' final fixture will secure a spot in the knock-out stages of the competition.
Gillingham had already qualified for the Second Round after winning their first three matches in Group 5, but that did not stop the Kent side from competing fiercely on a blustery day at Boots & Laces.
Hicham Abdellah replaced Fope Coker on the right-hand side of midfield in the only change from the side that drew 2-2 at Dagenham & Redbridge, with James Stevens returning in time from travelling to Iceland with the Northern Ireland Under-19 squad to participate. Goalkeeper Luke Chambers is currently in Lithuania with the Wales Under-17 set-up, meaning that he could not take up his spot on the substitutes' bench.
The strong cross-field wind meant that it took some time for either side to get into their stride, although Stevens went close with a twice-retaken set-piece drilled just wide of the left-hand upright in the third minute.
A Gills midfielder skewed over from 20 yards a little later in proceedings, but in general it was Southend who coped better with conditions in the opening period as they began to put together some intricate passing moves in the opposition half.
Duane Ofori-Acheampong went close on 23 minutes when he curled inches past the right-hand post on the turn, and he was denied by the Gillingham goalkeeper diving bravely at his feet shortly afterwards, George Smith having flicked Julian Okai's pass into his path.
Smith himself was thwarted by a smart save from the shotstopper on the half-hour as he attempted to head Anthony Furlonge's right-wing cross in from eight yards, but Blues would not have wait much longer to take the lead.
Abdellah again combined well with the overlapping full-back Furlonge to set his team-mate away on the right, and this time the first-year scholar galloped into the box, drawing a defender to him before squaring towards Ofori-Acheampong. A lack of communication at the back led to the visiting custodian colliding with a defender, and Ofori-Acheampong was left with the simple task of leathering the loose ball into an empty net from close range.
Five minutes later, Smith and Stevens combined to present Okai with an excellent opportunity one-on-one with the 'keeper, but he could not control his chipped finish and it sailed over. In the final action of the first half, Daniel Bentley was required to tip a swirling cross over from underneath his crossbar, although this was a rare threat from the Kent side.
Further intelligent passing from Smith around the opposition penalty area gave Stevens a chance to get a shot in on goal, but an additional touch before delivering his 51st-minute effort meant that a defender was able to get across to block.
Southend were almost gifted a second goal after 69 minutes when Ofori-Acheampong's well-struck shot was deflected towards the 'keeper. He spilled the ball and a defender's attempted clearance was smashed directly at a colleague, with the ricochet whizzing narrowly past the post.
Within seconds, a Gills forward had fired wide but, in general, Southend retained possession reasonably well in the closing stages to avert a repeat of last weekend's late drama.
There was, however, one nervous moment in the 89th minute when a fierce free-kick flew goalwards, but Bentley palmed the ball over his crossbar to maintain his own clean sheet and help his side claim the three points.
Southend United: Daniel Bentley, Anthony Furlonge, Teddy Nesbitt, James Stevens (Michael Hyland 77), Louis Baucutt, Kane Ferdinand, Hicham Abdellah (Rhys Mackay 64), Alex Woodyard, Duane Ofori-Acheampong, George Smith, Julian Okai (Ryan Auger 70).
Substitute not used: Jack Paxman.
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