The Gills were beaten 4-3 on penalties after Tuesday's Johnstone Paints Trophy game ended goalless.
Its not a game that will live long in the memory, the Gills failing to test home keeper Rhys Evans throughout the game but thankfully the spot-kicks certainly brought some excitement at the end of the 90 minutes.
Stefan and Jack Payne had their efforts saved while Saturday's hero Danny Spiller smashed his way over the top and although Lance Cronin made a couple of decent saves it was Southend manager Paul Sturrock's son Blair that netted the decisive one for the Shrimpers.
Not that Sturrock senior was watching, he admitted afterwards that he'd gone down the tunnel and sat alone in the dressing room ahead of the penalties.
Andy Hessenthaler made five changes from the team that started against Morecambe. John Nutter, Josh Gowling, Luke Rooney, Kevin Maher and Mark McCammon coming in for Chris Palmer, Matt Lawrence, Mark Bentley, Andy Barcham and Adebayo Akinfenwa. Of these only Barcham was amongst the substitutes.
Gills played a 4-4-2 formation, Rooney played at the point of the diamond behind the front two of McCammon and McDonald, Spiller and Payne gave very little width in a narrow midfield with Maher in the holding role. Barry Fuller was in his normal right-back position, Nutter and Gowling returned at left-back and central defence respectively with Tony Sinclair and Cronin making up the starting XI.
Southend had plenty of the ball in the early stages but it was Rooney that had the first shot of the night, it didn't trouble Evans in the home goal however.
A long throw from Payne caused the United rearguard problems, Rooney laid the ball back for Nutter to cross but although McDonald got in a header at the far post he couldn't guide it on target.
In the 18th minute Ryan Hall played a lovely ball into the area, Corr had to stretch his neck muscles to get a header goalwards which forced Cronin to touch over the bar.
Four minutes later, Hall, who played for Bromley in the pre-season friendly against the Gills, curled in a free-kick that just missed its targets in the middle and wasn't too far wide of Cronin's right-hand post.
McDonald went through the middle onto a Maher through ball, he went between Josh Simpson and Bilal Mohsni before going down a yard or two from the area. If he had whistled then Mohsni would probably have seen red. Referee Gavin Ward waved play on.
A flurry of chances then came at both ends. Sinclair had a shot blocked and Spiller saw a miscued shot cleared by Anthony Grant in front of goal while for Southend, Adam Bouzid got behind the Gills defence on the left, his low shot struck the feet of Cronin and flew to safety.
H/T: 0-0
Shrimpers boss Sturrock made two changes at the break, replacing Hall and Bouzid with Sofi Zaaboub and Louis Soares.
In the 52nd minute Maher struck a long range effort just wide against his former side. Then another free-kick routine involving Spiller, Rooney and Nutter ended with the latter's shot being deflected wide. From the resultant corner Spiller had a header blocked.
On the hour Barcham came on to replace Rooney but was limping within a minute following a heavy challenge. McDonald was also caught in a tackle and both had to leave the field following treatment.
While still struggling the on-loan Norwich striker was an inch away from reaching a Spiller cross but was limping even more heavily after landing. He was quickly replaced by Stefan Payne but Barcham, who was to leave the ground later on crutches, soldiered on.
Sturrock was put clear inadvertently when Fuller cleared from Matt Paterson but the strikers shot wasn't clean and Cronin was able to block.
Stefan Payne set up a chance for namesake Jack but the midfielders right-foot effort sailed over the 426 Gills supporters in the North Stand who once again provided great support, over the scoreboard and out of the ground.
Sinclair was booked for the third time this season pulling down a United player as he looked to break from midfield.
Referee Ward blew the final whistle and took the game to a penalty shoot-out..... which were taken in front of the empty Frank Walton Stand
0-0 The Gills didn't get off to the best of starts, Stefan Payne seeing his effort saved low to his right by the Evans.
0-1 Louis Soares puts Southend ahead, firing high to Cronin's left.
1-1 Mark McCammon levels the scores, sending Evans the wrong way.
1-1 Home skipper Craig Easton see's his strike down the middle kept out by Cronin's outstretched hand.
2-1 John Nutter confidently sends the keeper the wrong way.
2-2 Chris Barker reciprocates, his penalty and Cronin going different ways.
3-2 Kevin Maher keeps cool against his former side, Evans again choosing the wrong way.
3-3 Matt Paterson doesn't give Cronin a chance, smashing the ball high into the rigging.
3-3 Danny Spiller smashes the ball high over the top into the top tier of the stand.
3-3 Anthony Grant has his low attempt to Cronin's left well saved.
3-3 Jack Payne had problems with the spot prior to his penalty, his central strike is kept out by the keeper's right boot.
3-4 Blair Sturrock stepped forward to confidently beat Cronin.
A note for supporters interested in ex-Gillingham players - both Paul Clark and David Crown, former players of both sides, were in and around the press-box before kick-off.
Att: 3,073 (426 Gills)
United: Evans, Gilbert, Simpson, Mohsni, Grant, Easton, Corr (Paterson 64), Hall (Zaaboub H/T), Bouzid (Soares H/T), Sturrock, Barker.
Subs: Morris, Coughlan.
Gills: Cronin, Fuller, Nutter, Maher, McCammon, McDonald (S Payne 67), Rooney (Barcham 60), Gowling, Spiller, J Payne, Sinclair.
Subs: Julian, White, Essam.
