Pelle scored his first just before the half-hour mark largely thanks to poor defending from Ben Davies, before Erik Lamela levelled from close range in controversial fashion just before half-time.
Saints were ahead again on 65 minutes as Pelle rose above Federico Fazio to head home superbly, but Spurs equalised for a second time through Nacer Chadli’s neat finish from eight yards.
The result helps neither side in their race for the Champions League places with four games of the season remaining.
Spurs boss Mauricio Pochettino was given a heated reception by some Southampton fans on what they coined ‘Ronald Koeman day’, as the Argentine returned to St Mary’s for the first time since leaving the club for White Hart Lane in the summer.
The first clear opportunity of the game fell to the hosts, Hugo Lloris doing well to turn away Morgan Schneiderlin’s drive from a James Ward-Prowse corner, but Southampton took the lead on 29 minutes after a catalogue of defensive errors.
First, Ryan Mason slipped when attempting to clear after the visitors’ had snuffed out Saido Mane’s run, before Davies allowed Pelle to poke home from 12 yards despite the defender seemingly being in possession of the ball.
Steven Davis had the chance to double Saints’ lead shortly after, but the midfielder miscued from 16 yards after Ryan Bertrand’s centre.
But Spurs levelled through Lamela two minutes before the break, though there was a hint of handball as the Argentine looked to chest the ball goalwards after Harry Kane flicked on Eric Dier’s cross.
Davis had two more clear chances after the break to trouble Spurs goalkeeper Lloris, but he first dragged his effort wide from 20 yards, before missing the target from close range after a fine turn.
But the hosts finally turned their pressure into a second goal as Pelle produced a fine header from 12 yards to beat Lloris from substitute Shane Long’s cross.
Italian Pelle has now scored three goals in his last three games, having scored just one for Southampton in his previous 17.
But Spurs fought back to level for a second time through Chadli, who slotted into the corner from an angle after Dier’s fine through ball down the right channel.
Toby Alderweireld’s diving header in stoppage time was gratefully collected by Lloris and Jose Fonte’s header at the death flew just over, as Spurs held on for a point.
Southampton: Kelvin Davis (5), Clyne (6), Fonte (6), Yoshida (6), Bertrand (6), Schneiderlin (6), Alderweireld (6), Ward-Prowse (6), Mane (6), Steven Davis (5), Pelle (7).
Subs: Long (6), Elia (5), Reed (5).
Tottenham: Lloris (6), Dier (7), Fazio (5), Vertonghen (6), Davies (4), Mason (5), Bentaleb (5), Lamela (6), Eriksen (6), Chadli (6), Kane (5)
Subs: Chiriches (5), Soldado (5), Dembele (5)
Man of the match: Graziano Pelle