A dull opening hour was enlivened when Shaun Goater put the hosts ahead from the penalty spot, but the Tykes equalised through Marc Richards within two minutes.
The visitors nearly got a dream start when Richards set up strike partner Paul Hayes after just 43 seconds. His shot beat Darryl Flahavan's dive but hit the foot of the goalkeeper's left upright from 20 yards.
That was as good as it got for the Tykes until much later in the half as the high-flying hosts created the better chances with striker Freddy Eastwood providing the main danger.
Firstly his dangerous cross was headed out for a corner by centre-back Anthony Kay on eight minutes. From the resulting Kevin Maher flag-kick Shrimpers defender Adam Barrett headed directly at Nick Colgan.
Two minutes later Eastwood's centre from the left was met by veteran forward Goater but he could only head over.
Kay continued his heroics to keep Eastwood and Jamal Campbell-Ryce at bay before the winger's dash down the right ended with James Lawson being denied by Colgan's legs in first-half stoppage time.
Southend remained on top in the opening exchanges of the second period with Goater heading wide from six yards following a smart one-two between Luke Guttridge and Campbell-Ryce.
The hosts took the lead on 59 minutes from the penalty spot when Bobby Hassell was adjudged to have held down Goater as he attempted to jump to meet a Campbell-Ryce cross.
Referee Lee Probert pointed straight at the spot and Goater fired the spot-kick into the top left corner for his sixth goal of the season although Colgan guessed the right way.
But the lead lasted just two minutes as central midfielder Jacob Burns floated a free-kick in from the left and Richards got the slightest of touches with his head at the far post.
Barnsley could have made it two on 78 minutes as Brian Howard tried his luck from 25 yards with a powerful drive that Flahavan turned around his right post for a corner.