Southampton travelled to north London knowing a win would take them into at least second spot in National Group 2, but fell behind after 21 minutes as former St Mary's loanee Yago Falque curled past Chris Johns.
And the free-scoring hosts doubled their lead soon afterwards as Tom Carroll's cross found the head of Jon Obika, who powered home well.
Saints looked to have ended the opening period having found their feet, but were dealt a cruel blow inside added time as Falque excellently added his second by shooting in from the edge of the box via the crossbar.
The visitors had the better of the second half but failed to take their chances, and were further punished nine minutes from time by Spurs substitute Souleymane Coulibaly.
Spurs U21s: Vigouroux, Fredericks, Stewart, Luongo (c), Hall, Carroll, Falque, Mason, Obika, Parrett (Coulibaly 67), Ceballos (Pritchard 77). Subs not used: McGee (GK), Veljkovic.
Goals: Falque (21 & 45+1), Obika (24), Coulibaly (81)
Saints U21s: Johns, Butterfield, Mugabi, Turnbull, Targett (Young 79), Curtis (Gape 69), Moore, Reeves (c), Isgrove (Seager 11), Hoskins, Sinclair. Subs not used: Britt (GK), McQueen.
Referee: Mr S Butler
Assistant Referees: Mr S Barry & Mr P Evans
Fourth Official: Mr W Cartmel
U21s Coach Martin Hunter named perhaps his youngest starting XI of the season, with Danny Butterfield his only overage player.
With regular centre-back Jack Stephens away on international duty, Under-18s defender Bevis Mugabi was included along with 17-year-old Matt Targett.
Spurs, meanwhile, boasted a number of players who have spent time out on loan in the Championship such as Falque, Obika, Carroll and Ryan Mason.
The hosts went into the game having surged to the top of their group with a string of impressive victories, and certainly showed their quality from the off.
Tim Sherwood's men could well have gone ahead inside the opening 60 seconds when a ball from the right caused havoc in the Saints box, but Falque – who spent the first half of 2012 on loan at St Mary's – miscued his shot.
Then, two minutes later, a ball over the top from Spurs captain Massimo Luongo found Mason in a good position but his attempted chip was easily held by Chris Johns.
The visitors were dealt an early blow when winger Lloyd Isgrove – who made his first-team debut less than a fortnight ago – limped off to be replaced by Ryan Seager after 11 minutes.
That change sparked a flurry of chances, though, with Butterfield's low cross almost catching Spurs out as Ryan Fredericks was forced to bundle the ball behind with Seager lurking.
Barley a minute later, Tottenham left-back Kevin Stewart looked to have broken through the Saints defence only to be denied by a superb slide from Mugabi.
Jake Sinclair then saw a left-footed effort held by opposing 'keeper Lawrence Vigouroux, before Falque failed to make the most of a good opportunity when he shot into the side-netting.
Two excellent chances fell Saints' way just after the quarter-hour. First, a low delivery from left-back Targett was helped onto Sam Hoskins by Seager, but the prolific front-man shot inches wide.
Hoskins had another opportunity moments later as he picked up Corby Moore's pass and shook off two Spurs defenders, only to be denied from close range by Vigouroux.
Saints' failure to make the most of those chances was duly punished as a rapid break by the hosts saw the ball find its way to Falque, who delicately curled in a 21st-minute opener.
Hunter's men were caught cold, and Spurs duly doubled their lead on 24 minutes as Tom Carroll's right-wing cross was powered home by the head of Jon Obika.
The game quickly settled down soon after the home side's second, with Saints perhaps having the better of the play without carving out any concrete chances.
Seager found a way through the Spurs rearguard eight minutes before the break but his low delivery was seized upon by Vigouroux ahead of Sinclair and Hoskins.
Then, on the 45-minute mark, a long clearance by Mugabi looked to have played Sinclair in but the ball got caught under his feet and the home side managed to clear.
But, inside the two minutes of first-half injury time, Spurs dealt their opponents a hammer blow as the ball broke for Falque on the edge of the box, and the Spaniard duly curled in his second via the crossbar to close the opening period.
The second half started at a far slower pace than the first, with the only half-chance of the opening ten minutes going Spurs' way as Obika slammed wide of the near post after shaking off Mugabi.
Saints had the ball in the net just before the hour as Hoskins scooped the ball over Vigouroux and inside the far post, but the forward had already been declared offside.
The six-goal striker had another opportunity on 62 minutes after being played in by Seager but he failed to spot Matt Targett's lung-bursting run into a supporting position and instead fired over.
The visitors looked to have found a renewed energy, with Moore's shot being parried into danger by Vigouroux only for Seager to be flagged offside as he looked to follow up.
Cristian Ceballos – scorer of a hat-trick in last month's return fixture – then saw a free kick saved by Johns before Hoskins was again denied by Vigouroux at the end of a smart counter.
Hunter gave Under-18s captain Dominic Gape a debut at this level on 69 minutes, bringing on the central midfielder in place of Joe Curtis.
Saints continued to push for a consolation, with Seager and Moore both being denied by the seemingly-unbeatable Vigouroux.
Instead it was Tottenham who scored the game's fourth goal, with substitute Coulibaly firing beyond Johns from just inside the box before celebrating acrobatically.
Vigouroux's superb showing between the sticks continued into injury time, as he pulled of his best save of the evening to tip Ben Reeves's shot around the post and bring the game to an end.