The former MK Dons frontman struck just after the hour mark when he crashed in the rebound after Shrimpers keeper Rhys Taylor fumbled Elliot Lee's shot.
Nicky Maynard put the Hammers in front in the first half when he headed in Matt Taylor's corner and young right-back Jordan Spence drilled in the second before half-time.
The only sour note for boss Sam Allardyce was the sight of young left-back Dan Potts being stretchered off after an aerial challenge.
Former Hammers trainee Freddy Eastwood got a late run-out for Southend but could not manage to grab a consolation goal.
