Maya Yoshida scored the only goal of the game inside the first ten minutes with a close-range effort from Victor Wanyama's pass, before Wanyama was sent off early in the second half for a heavy foul on Dimitri Payet.
Saints strike after dominant start
It was the home side who dominated the early proceedings, winning a number of corners in the opening ten minutes, so it came as little surprise when they took the lead through Yoshida just before the nine-minute mark.
Sadio Mane fed Wanyama at the right side of the penalty area and the Kenyan midfielder got to the ball first to stab it into a dangerous area, where Yoshida was waiting to stab home only his third league goal for the club from the middle of a crowd at the edge of the six-yard box.
Southampton kept their foot on the pedal after taking the lead as Graziano Pelle went close twice soon after, while Victor Moses' deflected shot after 20 minutes was the first time the Hammers threatened in the game.
Reid misses chances to equalise
Enner Valencia had claims for a penalty waved away by Mark Clattenburg moments later, while Winston Reid was denied by a smart save from in-form Saints 'keeper Fraser Forster from Payet's free-kick into the area.
Five minutes later, Payet aimed for Reid again from another set piece, but the defender couldn't keep his header down and it sailed harmlessly over the crossbar.
The rest of the first half was devoid of any real goalscoring opportunities, with a number of bitty fouls from both sides ensuring a lack of rhythm or tempo to the game.
Valencia's low effort early in the second half was an improvement on proceedings as Forster got down well to save, but Southampton were a man down with less than ten minutes of the second period played.
Wanyama dismissed for crunching foul
Wanyama gave away possession in the centre of the park and made a desperate lunge on Payet to try and win the ball back, with the Hammers talisman requiring some attention from the club's medical team.
Tempers threatened to flare as captain Reid confronted Wanyama, but referee Clattenburg kept the situation in control and ejected the midfielder from the pitch. It was his third sending-off of the current season.
Ronald Koeman sacrificed the attacking flair of Mane as a result, bringing on Oriol Romeu to try and shore things up in midfield.
Shane Long and Alex Song went close for their respective teams as Wanyama's dismissal opened the game up, with Slaven Bilic introducing Andy Carroll and January signing Emmanuel Emenike to the fray in an attempt to force the issue as his side looked for an equaliser.
Southampton see out final stages
Fellow substitute Charlie Austin, making his home debut for Southampton, had an effort blocked by James Collins after a ball over the top from Romeu, while Song bent another effort wide as the game drew on into the final ten minutes.
Valencia fired a free kick over the crossbar from range after Emenike was brought down 30 yards from goal, but West Ham failed to test Forster in five minutes of stoppage time and the Saints clung on for the win.
Bilic's men retain their position in the top six of the Premier League, but the three points see Southampton leapfrog the two Merseyside teams Liverpool and Everton into seventh, one place and two points behind the Hammers.