Blues exited the Emirates FA Cup at the second-round stage as Chris Powell’s side lost 4-2 to Barnsley at Roots Hall.
Kieffer Moore put the visitors in front with his fifth goal in three games against Southend midway through the first-half, powering a header home from an Alex Mowatt corner.
Southend would level though right on half-time when Sam Mantom’s corner appeared to go all the way through and into the back of the net to make it 1-1 at the break.
Barnsley retook the lead early in the second-half when Blues failed to deal with another set-piece from Mowatt, allowing Cauley Woodrow to score from close range.
And the former Southend-loanee would put daylight between the two sides by tapping in Mike Bahre’s cross-come-shot after Blues again failed to deal with a corner.
Southend would give themselves hope of staying in the competition when Timothee Dieng headed in Stephen McLaughlin’s corner before Blues thought they’d equalised in the final minute of normal time only for Michael Turner’s strike to be controversially ruled out for offside.
It didn’t matter in the end though as Barnsley wrapped up the win in the fifth minute of stoppage time after George Moncur’s effort was parried to Bahre who fired in a fourth for the Tykes.
The win for the visitors sees them go into the hat for Monday’s third-round draw while Southend must now concentrate on improving their league fortunes.