The 30-year-old striker scored from close range in the 35th minute after good work on the left from 17-year-old Glenn Johnson to continue the reserves' 100% home record at Dagenham & Redbridge's Victoria Road ground this season.
The goal was just rewards for an impressive first half performance from the Hammers, after Shaun Byrne, Svetoslav Todorov and Shaun Byrne had all gone close to opening the scoring.
Southampton came to life after the break and had chances of their own to draw level, although the Hammers never looked in serious danger of surrendering their lead.
Manager Roger Cross fielded a 3-5-2 formation, containing a healthy blend of experience and youth, and it was the young midfield of Johnson, Byrne, Leon Britton, Richard Garcia and Adam Newton that caught the eye.
Said Roger afterwards: "It was a tough game and we played very well in the first half. We created a number of good chances and should really have come in two or three up at half-time.
"It's always hard when you don't get the second goal, though, and they improved a lot in the second half, closing us down quickly and making it a lot tougher for us.
"You're never relaxed until the second goal goes in but I was generally pleased with the performance, especially from the young lads in midfield.
"We asked Leon Britton to play a holding role, allowing Richard Garcia and Shaun Byrne to get forward, but they all helped each other out.
"And young Glenn Johnson played very well - he is going to be a very good player for this Club in the future."
The match provided the first taste of action for the reserves since September 4, and Roger admitted that he was glad to get back in the swing of things.
"It's been three weeks since the last game so it was nice to get back out there tonight. We've got a nice mix of young and senior players who are all hoping to impress the first team manager, so we can hopefully look forward to a successful season."
Team: Forrest, Potts, Foxe, Soma, Newton, Johnson, Britton, Byrne, Garcia, Todorov, Kitson. Unused subs: B.McMahon, Ferrante, U'ddin, Clark, Cascione.