The forward, on loan from Reading, netted with a fine 12-yard header from Charlie Mulgrew's free-kick from the right in the fifth minute of first-half stoppage time, although only four minutes had been indicated by the fourth official.
The goal cancelled out Jason Scotland's penalty which was awarded after Mulgrew tripped Thomas Butler as he ran into the Southend box.
Scotland sent Shrimpers keeper Darryl Flahavan the wrong way as he slotted the ball into the right side of the net - his 26th goal of the season.
In an evenly contested match, Peter Clarke went close to scoring twice with headers for Southend, while substitute striker Lee Barnard shot wide when clear through on goal following Ferrie Bodde's error.
The Shrimpers had a good shout for a penalty turned down by referee Pat Miller when Barnard had his shirt tugged by Darren Pratley in the 18-yard-box.
Thomas Butler twice had the Southend defence on the rack with his fine approach play but both times his shots failed to cause Blues goalkeeper Flahavan any problems.
But the woodwork came to the hosts' rescue when Bodde hit the crossbar midway through the second half.
And Nicky Bailey ensured a share of the spoils for play-off hopefuls Southend when he cleared Kevin Austin's back-heel off the line following a spell of sustained Swansea pressure.