Dean Cox put the visitors in front before goals from Billy Paynter, Lewis Hunt and Freddy Eastwood in a four-minute spell put the Shrimpers in the driving seat before Adam El-Abd pulled a goal back.
After a fairly even start it was Brighton who had the first meaningful chance.
French forward Alex Frutos squared the ball to Tommy Fraser, who was prevented from shooting by Adam Barrett and opted to pass to Alex Revell, but his angled drive went wide.
Southend then hit back with a cross-field ball from Simon Francis finding Mark Gower on the left, but his 20-yard effort was straight at Seagulls keeper Michels Kuipers.
A dull midfield duel was enlivened on 22 minutes when midfielder Cox chanced a snap-shot from 25 yards that went wide.
He repeated the feat 18 minutes later after Shrimpers skipper Kevin Maher scuffed an 18-yard effort wide of the target.
The Championship hosts finished the half with a flourish as Eastwood's shot was parried by Kuipers and cleared by Joel Lynch only for striker Paynter to head Gower's cross straight at the Dutch custodian from four yards.
The League One visitors came close to break the deadlock two minutes after the restart when Gary Hart fired into the side netting from Revell's cross.
Southend lifted the tempo and were nearly rewarded when five-goal top scorer Eastwood headed inches over the bar following a Francis centre.
The Shrimpers maintained their pressure and caretaker Seagulls manager Dean Wilkins introduced Doug Loft for Frutos after 69 minutes.
The substitution paid dividends three minutes later when the midfielder set Cox up and the forward curled a fine strike from the edge of the box beyond a diving Darryl Flahavan.
Southend started their recovery on 86 minutes when a Hammell corner was nodded on by Hunt for Paynter to head home his first goal since signing from Hull.
A minute later Southend took the lead when Hunt fired in a 25-yard left foot volley before Eastwood grabbed a third in stoppage time with a 20-yard drive.
But Brighton were not finished and pressed for extra-time after Cox's free-kick was headed home by El-Abd.