Hosts Spurs moved into a 2-0 lead after first-half goals from Tynan Thompson and Lucá Williams-Barnett, but Saints halved the deficit by half time through Sufianu Sillah Dibaga.
Saints took control in the second period though and were level through Korban McMullan shortly after the break, and further strikes from Nick Oyekunle and Harry Gathercole confirmed the win.
The first opening of the game came for Saints inside the first 10 minutes when Dibaga cut the ball back for McMullan to strike goalwards, but his effort – destined for the bottom corner - was well blocked by Spurs.
However, Spurs gained the lead in the 17th minute when a seemingly dubious penalty was awarded to them and Thompson converted the spot-kick confidently.
Saints looked for a way back into proceedings as the game moved past the half-hour mark, and Aston Daley found space outside the Spurs area to fire in a left-footed shot that flew wide of the far post.
A good spell for Saints proved unfruitful though and this allowed Spurs to double their lead with a brutal counter attack as Williams-Barnett broke through and slipped a smart finish past Saints goalkeeper Dylan Moody.
Saints goalscorer Harry Gathercole in action
Andrew Surman’s visitors did manage to half the deficit before the half-time interval as a good response to the second Spurs goal saw Dibaga get on the scoresheet with a well-taken goal on 44 minutes.
A great start to the second half saw Saints follow up their strong end to the first period and find an equaliser in the 49th minute.
Gathercole was played in behind the Spurs defence on the left and, having drawn home keeper Samual Archer off his line, laid the ball back for McMullan, who clipped a delightful finish in via the far post with three Spurs defenders heading back onto the goal line.
The contest was finely poised heading into the final 15 minutes, with both sides going close to a third goal – Ellis Lehane heading a cross wide from a promising position and McMullan heading straight at Archer at the other end.
However, Saints did manage to complete a brilliant turnaround when Oyekunle, introduced at half time, had a hand in two goals that secured the three points for Saints.
The striker made it 3-2 himself by controlling and placing left-footed into the far corner on 75 minutes, and he turned provider just four minutes later when he played Gathercole into a shooting position – the latter finding the perfect finish across goal to give Archer no chance.
Saints are back in action on Saturday 8th March when they take on Brighton and Hove Albion in the Under-18 Premier League, with kick off at Staplewood set for 11am.
Tottenham Under-18s: Archer, Upson, Byrne, Byfield (Furnell-Gill 78), Hardy (Oliver 80), Hall (Batty 55), Elliot-Parris, Bangura (Logan 87), Lehane, Williams-Barnett, Thompson.
Subs not used: Irow.
Goals: Thompson (17’ pen), Lucá Williams-Barnett (38’).
Yellow cards: Bangura.
Southampton Under-18s: Moody, Adjei-Afriye (Newman 82), Dobson-Ventura (c), Okonola-Matthews, Sewell, Martin, Dibaga (Myers 83), Daley (Rodda 45), Gathercole, McMullan, Goremusandu (Oyekunle 45).
Subs not used: Abbotson.
Goals: Dibaga (44’), McMullan (49’), Oyekunle (75’), Gathercole (79’).