Steven Davis’ brace earned Southampton their first league win at White Hart Lane since 2003.
A persistent Son Heung-min gave Spurs a 1-0 lead on 16 minutes when he rounded a helpless Fraser Forster before slotting into an empty net.
But Davis drew the visitors level turning in Dusan Tadic’s cross at the near post.
Davis then netted the winner with a shot from the edge of the box after Jan Vertonghen saw his header cleared off the line at the other end.
Jose Fonte blocked substitute Nacer Chadli from putting his attempt on goal late into stoppage time as Spurs looked to salvage a point.
Southampton climbed into sixth place ahead of West Ham who has a game in hand.
Tottenham: Lloris (c), Walker, Alderweireld, Vertonghen, Rose; Dier, Mason (Chadli 78), Lamela, Eriksen, Son (Clinton 65), Kane.
Unused subs: Vorm, Davies, Wimmer, Carroll, Winks.
Goal: Son (16).
Southampton: Forster, Martina, Fonte (c), Van Dijk, Bertrand, Clasie (Romeu 58), S.Davis, Wanyama, Tadic (Ward-Prowse 86), Mane (Pelle 65), Long.
Unused subs: Stekelenburg, Cedric, Yoshida, Austin.
Bookings: Mane, Romeu, Long.
Goals: Davis (31, 72)