Ten man Southend United snatched all three points at the death with Mark Phillips bagging the winner for the home side.
Bilel Mohsni had seen red for a second bookable offence in the 66th minute and the Gills thought they must have been in with a chance of winning the game, but Phillips’ header from a corner made it four games without a win for Andy Hessenthaler’s side.
Before the late drama, both sides had found it tough to create clear cut chances. Gillingham, wearing their pink kit, had made just the one change to the side that drew with Accrington at the weekend with Danny Spiller replacing Lewis Montrose in midfield.
But, with seven minutes on the clock, Luke Rooney burst in to the Southend penalty area and saw a well struck shot smartly saved to his left hand side by Blues goalkeeper Glenn Morris.
Southend hit back and almost opened the scoring themselves in the 14th minute of the match when a left wing cross from the recalled Peter Gilbert was headed in to the path of Blair Sturrock by Mohsni and the striker cushioned a volley against the crossbar from 14 yards.
Moments later, a scorching 30 yard shot from Hall was comfortably kept out by Gillingham keeper Ross Flitney before the visitors’ Joe Martin forced Morris in to action with a similar effort at the other end of the pitch.
On the stroke of half-time, Danny Spiller fired just wide of the left post from the edge of the penalty area, meaning the game remained goalless at the break.
At the start of the second period, an under pressure Kane Ferdinand stabbed a deep right wing corner from Hall over the crossbar at the back post before Gills midfielder Danny Jackman sent a 20 yard volley looping just inches over the crossbar.
In reply, Mohsni then sent a long range effort straight at Flitney in the 53rd minute of the match before the Frenchman was shown his first yellow card of the evening.
The striker fell the floor while racing alongside former Southend centre-back Garry Richards and referee David Phillips immediately cautioned him for diving.
Following that, the Gills soon hit back with Morris again doing well to parry away a well struck shot from Rooney.
But Southend should then have opened the scoring when a left wing free-kick from Hall picked out an unmarked Phillips six yards from goal.
However, the centre-back appeared to mistime his jump and the ball flew harmlessly over his head.
After the wasted opportunity, Blues were reduced to 10 men in the 66th minute when Mohsni was shown a second yellow card after intentionally getting in the way of a Richards free-kick.
Gillingham almost made the most of their extra man in the 74th minute when Morris impressively kept out a deflected drive from Danny Kedwell and the keeper did well again to keep out substitute Stefan Payne 10 minutes later.
Morris denied the same player again in the 86th minute and, just 60 seconds later, Southend bagged a late winner as Phillips’ near post header from Hall’s right wing corner crashed in to the back of the net via the underside of the crossbar.
FULL TIME: SOUTHEND UNITED 1-0 GILLINGHAM
Tuesday night’s defeat sees Gillingham slip to 13th in League Two with a trip to 23rd placed Hereford United to come on Saturday.
Southend line up: Morris, Clohessy, Gilbert, Bilel, Phillips, Barker, Hall, Grant, Timlin, Ferdinand, Sturrock (Prosser 94).
Subs not used: Bentley, Leonard, Johnson, Kalala.
Goal: Phillips (87).
Booked: Timlin (12), Bilel (54), Hall (72), Grant (76).
Sent Off: Bilel (66).
Gillingham line up: Flitney, Fuller, Richards, Lawrence (Montrose 73), Martin, Whelpdale (Oli 62), Lee, Jackman, Spiller (S Payne 76), Rooney, Kedwell.
Subs not used: Fish, Essam.
Booked: Kedwell (13), Fuller (68).
Referee: Mr Phillips
Attendance: 4,598 (550 Gills)