Jabo Ibehre's late goal earned Leyton Orient a point in a pulsating game.
Wayne Corden struck a post for the O's early on but the visitors took the lead when Orient failed to clear a cross and Lee Barnard scrambled the ball home.
Adam Boyd drew Orient level from the spot after Simon Francis handled but Southend regained the lead when Peter Clarke unleashed a superb 30-yard shot.
Tamika Mkandawire hit the bar for the O's before Ibehre struck, heading home Charlie Daniels' cross in injury-time.
Leyton Orient: Nelson, Purches, Saah, Mkandawire, Daniels, Melligan (Gray 67), Demetriou, Terry, Corden (Ibehre 68), Boyd, Barcham.
Subs Not Used: Morris, Oji, Palmer.
Goals: Boyd 51 pen, Ibehre 90.
Southend: Flahavan, Francis, Barrett, Clarke, Mulgrew, Black (Robson-Kanu 78), McCormack, Bailey, Gower, Barnard (MacDonald 46), Revell.
Subs Not Used: Collis, Hunt, Moussa.
Booked: Gower, Flahavan.
Goals: Barnard 27, Clarke 56.
Ref: Danny McDermid (England).