The Shrimpers were on top for prolonged periods at Roots Hall but were unable to find a way past Seagulls goalkeeper Niki Maenpaa.
And the Championship club capitalised by bagging a last-gasp winner, with LuaLua on target.
Before that late drama, Brighton had come close to bagging an early opener when Danny Holla’s 25-yard free-kick was parried around the left post by the Shrimpers’ highly-rated goalkeeper Daniel Bentley.
Southend hit back after the break and should have opened the scoring when a free-flowing move resulted in Ryan Leonard heading John White’s chipped right-wing cross wide of the left post.
With the home side remaining on top, substitute Myles Weston soon also came close to scoring when his well-struck 16-yard shot was smartly smothered by Maenpaa diving to his left-hand side.
But the Seagulls shot-stopper then pulled off a stunning save in the 87th minute when he somehow pushed a well struck 25-yard effort from Anthony Wordsworth wide of the right post.
The save proved to be crucial as Brighton immediately responded to bag an injury-time winner when Holla played in LuaLua, who raced in behind White before coolly firing past the advancing Bentley with an assured low shot.