There can be no faulting the effort of the side throughout the match, but goals at crucial times from the visitors, together with their determination not to give up their advantage meant we couldn't turn it around.
It didn't take long for the Saints to take the lead, just three minutes were on the clock when Matt Oakley's corner was met by Beattie and his header hit the far post and went in.
We almost had an instant response just two minutes later, when Rohan Ricketts picked up the ball and chipped in a delightful cross which Fredi Kanoute headed goalwards, only for his effort to beat Paul Jones but bounce off the crossbar and behind.
Jamie Redknapp's persistence nearly led to an equaliser on 13 minutes as he won the ball back out on the left and sent over a low cross and Claus Lundekvam's outstretched leg nearly beat his own goalkeeper, but Jones scrambled it away for a corner.
Saints were causing problems of their own however and Goran Bunjevcevic and Anthony Gardner both made smart clearances from dangerous crosses from Fabrice Fernandes and Graeme Le Saux respectively.
Redknapp's determination to lead by example and get us back in the game led to a booking on 22 minutes for a foul on Oakley, while Stephen Carr and Kevin Phillips both then sent low efforts just wide for either side.
Kanoute looked lively throughout the match and was a constant thorn in the side of the Saints defence. His touch was superb at times, he won most things in the air and he was quite rightly voted the spurs (((on!))) man of the match.
But we were two goals down just before the break when Beattie was awarded a harsh free-kick following slight contact with Ricketts 25 yards out and he made the most of the opportunity, drilling home the set-piece with real venom past Kasey Keller, who did well to reach the shot but couldn't keep it out.
Bobby Zamora then tested Jones with the final piece of action of the first half, his 25 yard shot forcing the Welsh international to parry away for a corner.
In an attempt to overturn the deficit, we made two changes at half-time with Robbie Keane making a welcome return from injury to replace Zamora, while Darren Anderton came on for Stephane Dalmat.
The second half began with Phillips hitting the crossbar and Kanoute sending a Mauricio Taricco cross just over, before a flurry of activity on the hour mark saw two goals in as many minutes.
First the visitors extended their lead, when Phillips converted Le Saux's low cross after a quick break following a spell of pressure from us.
But we hit back immediately when Keane found himself in acres of space down the left, he burst into the area and rolled the ball across for Kanoute to tap home his fourth league goal of the season.
That gave our crowd something to cheer about and the confidence in the side rose immediately. Just a minute later Keane almost wriggled through in the area but the Saints defence cleared.
A change in formation followed, with Helder Postiga replacing Bunjevcevic as we switched to 4-3-3 and the impetus was certainly with us at that stage, although clear cut chances were hard to come by.
Postiga sent a drive from the edge of the box wide from Kanoute's lay-off and Anderton's long-range free-kick was blocked by a Saints defender as we worked hard to try to turn the game around.
But the visitors were proving difficult to break down with a packed defence and indeed it was Phillips who had the best chance to score. He found himself clean through with just Keller to beat but as he rounded our American stopper, Carr had raced back to block and the striker's shot just clipped Carr and onto the bar - a great piece of defending from the full-back.
Ricketts then saw his attempted chip clear Jones' crossbar as we continued to battle away but, despite our best endeavours, there was to be no comeback.
Minute by minute guide
2 mins GOAL Oakley's corner headed in off the post by Beattie. 0-1
5 mins Kanoute headed against the bar from Ricketts cross.
13 mins Redknapp hassled, won ball back and crossed, Lundekvam's intervention had to be turned around post by Jones for corner.
14 mins Bunjevcevic stretching clearance as Phillips prepared to pounce on Fernandes cross.
18 mins Le Saux's dangerous centre cleared by Gardner's diving header.
19 mins Kanoute denied by Svensson's sliding challenge in the area.
22 mins YELLOW Redknapp booked for foul on Oakley.
33 mins Kanoute break down right, his cross led to goalmouth scramble before Saints cleared.
35 mins Again Kanoute instrumental, laying ball off to Taricco before continuing his run into box and meeting the cross, only for header to go well wide.
36 mins Carr bursting down the right, cut inside and fired low shot just past the near post.
37 mins Phillips moving into space but his 20 yard drive went wide of the mark.
42 mins GOAL Beattie again, this time from 25-yard free kick into the top corner, Keller hand to it, but couldn't keep it out. 0-2
44 mins Fine effort from Zamora from 25 yards, Jones diving save for a corner.
45 mins Half-time Spurs 0 Southampton 2.
46 mins SUB Half-time change for Spurs, Anderton on for Dalmat and Keane on for Zamora.
49 mins Beattie free-kick from 30 yards straight at Keller this time.
52 mins Fernandes break down the right, low centre between defence and keeper, Phillips sent his effort onto the bar and away for goalkick.
54 mins Taricco centre met by Kanoute but his header over the bar.
56 mins Le Saux long-range effort bounced off body of Keller but well clear of any danger.
58 mins Good spell of possession ended with Anderton's deep cross just out of Kanoute's reach.
60 mins GOAL Saints break, Marsden to Le Saux, his cross turned in by Phillips. 0-3
61 mins GOAL Break down the left from Spurs, Keane rolled ball across area for Kanoute to tap home. 1-3.
63 mins Keane almost through but Saints scramble ball away for corner.
64 mins SUB Postiga on for Bunjevcevic. Formation change to 4-3-3.
67 mins Postiga laid ball back to Kanoute, his drive from 18 yards just wide.
69 mins Anderton floated free kick flicks off Richards' head but wide.
71 mins SUB Anders Svensson on for Fernandes.
73 mins Anderton free-kick from 30 yards blocked by the defence.
76 mins Ricketts one-two with Kanoute, his cross-shot cleared for a corner.
81 mins Postiga fierce half-volley from right side of the area well saved by Jones before being cleared by defence.
82 mins Phillips clean through, rounded Keller, empty net in front of him but as he shot, Carr came back to block and his slight touch sent it on to crossbar.
84 mins SUB Prutton on for Marsden
90 mins Kanoute knock down for Ricketts but he couldn't keep down his difficult attempted chip.
Final Score - Spurs 1-3 Saints
A battling second-half performance wasn't enough to prevent us slipping to our second home defeat of the season after a James Beattie first-half double left us with too much to do.