Leyton Orient exited the Johnstone's Paint Trophy at the semi-final stage after John Egan's late winner sent Gillingham into the Southern Area Final.

Former Sunderland defender Egan got the decisive goal with ten minutes remaining when he headed home a corner – his third goal in two games for the Gills.

Mauro Milanese made five changes to his starting XI, only one of which – Andrea Dossena – was enforced. The Italian full-back missed out with injury, whilst skipper Nathan Clarke was rested and Dean Cox dropped to the bench.

In came Shane Lowry, Gary Sawyer, Romain Vincelot, Jobi McAnuff and Gianvito Plasmati. Wolverhampton Wanderers’ loanee Jack Price returned to his parent club during the week, whilst Cox and Dagnall also missed out.

Adam Legzdins started in goal, protected by a back four of Elliot Omozusi, Scott Cuthbert, Lowry and Sawyer. Bradley Pritchard, Josh Wright, Vincelot and McAnuff made up the midfield, with Gianvito Plasmati and David Mooney up front.

The hosts sprung a surprise by beginning in a 5-3-2 system which saw Jake Hessenthaler and Adam Chicksen utilised as wing backs.

Neither side was able to carve out a noteworthy chance in the opening quarter of an hour, though Plasmati did head tamely into the palms of Stuart Nelson thanks to sheer force of will.

The game gradually began to show signs of life after 20 minutes as Orient carved out two chances in quick succession.

Left-back Sawyer created the first with a floated right-footed cross which Mooney headed into the palms of Nelson, before Lowry tried his luck with a free kick the goalkeeper always had covered.

The best chance of the half went Gillingham’s way five minutes before half time. A free-kick into the penalty area fell to the unmarked Brennan Dickenson at the back post but Lowry blocked the forward’s shot superbly.

Seconds later O’s stopper Legzdins was lucky not to be giving his marching orders when he lost possession trying to be too clever on the ball. The gloveman attempted to rectify the situation by pulling Dickenson back, but referee Trevor Kettle was unmoved.

Just before the break Orient had their best chance; Plasmati forcing Nelson into an agile stop with a header from McAnuff’s free-kick delivery.

The first chance of the second period came as a result of another piece of unconvincing goalkeeping from Legzdins, who raced off his line to collect the ball but instead collided with Cuthbert and Dickenson, allowing the latter to cross behind Bradley Dack.

Much like the first half, chances were at a premium and when a cross from the right found Luke Norris on the far left of the penalty area, the striker perhaps ought to have taken a touch instead of ambitiously volleying over first time.

With little over 20 minutes remaining, Milanese’s side should have taken the lead when Pritchard met Sawyer’s left-wing delivery at the back post, somehow stabbing wide.

Captain Cuthbert came close soon after when he headed wide from a corner as Orient finally began to ask some questions of Peter Taylor’s side.

With 11 minutes remaining the home side looked set to open the scoring when substitute Cody McDonald took aim from a low cut-back from the right but saw his shot trickle agonizingly wide thanks to a deflection.

However from the resulting corer, Egan climbed highest to thump a header beyond Legzdins and hand Gillingham the lead.

With six minutes remaining Pritchard inexplicably missed the chance to pull Orient level when he somehow failed to convert substitute Shaun Batt's wicked left-wing cross.

In four minutes of stoppage time all the O's could muster was a blast from Omozui from distance as Gillingham secured their place in the Southern Area Final against either Coventry City or Bristol City.

Leyton Orient: Legzdins; Omozusi, Cuthbert, Lowry, Sawyer; Pritchard (Kashket 90), Wright, Vincelot, McAnuff (Cox 80); Plasmati (Batt 72), Mooney.

Subs: Grainger (GK), Baudry.

Gillingham: Nelson; Hessenthaler, Egan, Ehmer, Legge, Chicksen; Doughty, Loft (McGlashan 73), Dack; Norris (McDonald 73), Dickenson.

Subs: Morris (GK), Pritchard, Hoyte.

Referee: Trevor Kettle.

Attendance: 3,103 (620 away supporters).