The in-form striker bagged an unlucky 13th goal in as many Premiership games to snatch the points after we'd dominated proceedings for the first 20 minutes of the second half.
We created a host of chances in that period but Niemi stood firm to deny Robbie Keane twice and Teddy Sheringham twice, the most impressive to divert Sheringham's sidefoot effort with his legs.
The game always had an edge without any real pattern with football tricky on a sticky middle area of the surface.
Both defences impressed in the first half as few clear-cut chances were created.
Our first chance arrived after just a minute as Sheringham glanced Carr's free-kick inches wide.
Delap fired into the crowd after our best spell of possession and Telfer's 20-yarder produced the first save of the encounter as Keller tipped aside.
Perry, typically of the first half, blocked well as Ormerod latched onto a loose ball and Niemi got down well to smoother Carr's effort after the lively wing-back cut in from the left.
Keller got his angles right to block Delap's effort and Bridge's teasing cross skidded dangerously across the six-yard line as the half remained goalless.
The second half was a different story as we created a hatful of chances only to be denied by Niemi.
Again, it took only a minute for the first chance to arrive as Keane found a yard of space in the penalty area only for Niemi to save with his legs.
In the next 20 minutes King flicked Carr's corner just over and Keane fired a yard wide after making something out of nothing.
Niemi then comfortably dealt with Keane's free-kick, denied Sheringham a tap in by flicking Iversen's knock down away at full stretch and the pick of the bunch, another save with his legs to divert Sheringham's calculated attempt from 12 yards.
Gus Poyet and Darren Anderton's arrival off the bench signalled our attacking intent but there was a warning at the other end as first Beattie and then Tessem might have done better with headers.
Then the crucial blow. Beattie latched onto a ball over the top, cut into the box, across Richards and planted the ball into the bottom corner.
MINUTE BY MINUTE GUIDE
1min: CHANCE. Sheringham glanced Carr's free-kick just wide.
17mins: Delap break and wayward shot from 25 yards after our best spell of possession.
20mins: Telfer drive from 20 yards forced first decent save of the game from Keller to his left.
23mins: Iversen failed to clear convincingly but Perry there to block tackle Ormerod's half-chance.
24mins: After claims for handball turned down, Carr played in by Sheringham, cut in on left foot but Niemi smoothered low down.
25mins: Break up other end but Keller stood firm at near post to deny Delap.
29mins: Low cross from Bridge into danger corridor across six-yard line but no-one there to finish.
Half-time: Saints 0-0 Spurs
Half-time: SUB. Tessem for Ormerod.
46mins: CHANCE. Keane found a yard in the box but Niemi blocked with his legs.
48mins: Delap effort from 20 yards straight at Keller.
52mins: CLOSE. King flicked Carr's inswinging corner just over.
55mins: Bridge blaster from 25 yards taken at second attempt by Keller.
58mins: CHANCE. Keane made King's clearance into chance, taking the ball across Lundekvam and into box but Svensson back to help, left foot shot from 15 yards just wide.
62mins: Keane's free-kick dealt with comfortably by Niemi.
63mins: SAVE. Bunjevcevic's deep cross met by Iversen, knock down would have left Sheringham with a tap in but Niemi dived full length to divert ball away.
65mins: SAVE. Keane slid in Sheringham but sidefoot from 12 yards saved by Niemi's legs.
67mins: SUBS. Poyet for Bunjevcevic, Anderton for Taricco.
70mins: Beattie onto Tessem's deep cross but could only head straight at Keller from tight angle.
75mins: Tessem headed Fernandes cross over from 12 yards.
81mins: GOAL. Beattie latched onto ball over the top, cut inside Richards and tucked ball into bottom left corner. 0-1.
86mins: SUB. Acimovic for Iversen.
89mins: Acimovic played couple of one-twos but weak shot saved by Niemi.
Injury time: SUB. Davies for Fernandes.
Line-ups: Southampton: Niemi, Bridge, M Svensson, Lundekvam, Telfer, Oakley, Marsden, Delap, Fernandes, Beattie, Ormerod (Tessem, 45). Unused subs: Jones,Williams, A Svensson.
Spurs: Keller, Perry, Richards, King, Carr, Iversen, Freund, Bunjevcevic (Poyet, 67), Taricco (Anderton, 67), Keane, Sheringham. Unused subs: Sullivan, Thatcher.
James Beattie dealt us a huge blow after Antti Niemi kept us at bay at rain-lashed St Mary's.