Barnsley have now lost their last three Sky Bet League One games after slipping to defeat at in-form Southend.
The recalled Josh Scowen fired the Reds into the lead in the first half, but Phil Brown’s recovered and they secured a deserved fifth win in their last six games.
Barnsley threw away a lead before going in at half-time behind at Roots Hall following what proved to a be a feisty opening 45 minutes.
Manager Lee Johnson had made three changes to his starting line-up.
Looking to end a run of back-to-back league defeats, Johnson drafted Josh Scowen and Dan Crowley back into the midfield, while Michael Smith was given the nod up front.
He replaced Sam Winnall as the lone front-man, while Kadeem Harris was dropped to the bench and Conor Hourihane missed the clash at Roots Hall due to injury.
The visitors had the ball in the Southend net in the opening five minutes, only for Dan Crowley’s effort to be ruled out thanks to an offsideflag.
The Reds went in front after 24 minutes from the penalty spot.
Shrimpers’ goalkeeper Dan Bentley upended Marley Watkins as he skipped into the box, with referee Mr Breakspear pointing straight to the spot.
Up stepped Scowen to send Bentley the wrong way and at that point prospects looked rosy for Lee Johnson’s side.
However, Southend levelled in the 36th minutewhen Anthony Wordsworth drilled home after meeting a neat lay-off from Myles Weston.
The hosts then roared into the lead two minutes before the break when Luke Prosser tapped home from close range after latching on to a deflected cross from Weston.
The Reds pushed valiantly for an equaliser in the second period, but despite efforts from Alfie Mawson and sub Sam Winnall being saved, they couldn’t find that elusive point-saver.
Southend secured their first win against Barnsley since 1995.
Southend (4-4-2): Bentley; White, Bolger, Prosser, Coker; Leonard, Wordsworth, Timlin, Weston; Pigott, Mooney.Subs: Smith, Payne, Atkinson, Hurst, McLaughlin, Rea, Williams.
Barnsley (5-4-1): Davies; Wabara, Roberts, Mawson, Nyatanga, G Smith; Scowen, Pearson, Crowley, Watkins; M Smith.Subs: Townsend, Winnall, Harris, Digby, Bree, White, Jackson.
Referee: Charles Breakspear (Surrey).