Substitute Jack Clarke lashed Ipswich level in the 87th minute after goals from Southampton's Ryan Manning and Cyle Larin overturned Wes Burns' opener.
The South Coast stalemate moves Kieran McKenna's side a point clear of third-placed Millwall going into the final day of Britain's Championship season.
Despite stretching their unbeaten run to 18 league games, fifth-placed Southampton must be content with a place in the play-offs on the back of Saturday's agonising FA Cup semi-final loss to Manchester City.
Ipswich host QPR on Saturday, while promotion rivals Millwall, whose goal difference is inferior by 17, play at home to relegated Oxford.
Middlesbrough also remain in the hunt to finish runners-up to title winners Coventry and will go to play-off-chasing Wrexham at the weekend sitting two points off the pace.
In a tense tussle between two teams relegated from the top flight last term, Ipswich had the better of limited first-half chances on Tuesday (Wednesday AEST).
Ipswich winger Jaden Philogene twice tested Saints goalkeeper Daniel Peretz, while Ivan Azon also threatened.
Recalled Southampton striker Larin curled narrowly over for the hosts and later directed a tame header straight at Tractor Boys keeper Christian Walton.
Larin tested Walton with an acrobatic effort within a minute of the restart, before Ipswich edged ahead in the 48th minute.
After Jacob Greaves dispossessed Tom Fellows in midfield and lifted the ball over the top, Azon poked across the box for Burns to lash beyond Peretz.
Ipswich's sold-out away end was sensing a crucial victory, but the advantage lasted only 10 minutes.
Greaves was booked for a lunging challenge on Finn Azaz just outside the Town box, and from the resulting free-kick Manning's low effort flicked off Marcelino Nunez to fly into the roof of the net via the leg of the wrong-footed Walton.
Azaz drilled wide, before a moment of magic turned the match in the home side's favour in the 80th minute.
Manning drove forward and slid a pass into Canada international Larin, who calmly stepped inside Greaves and Leif Davis to stab the ball beyond Walton.
A four-way final-day promotion shoot-out was on the cards, but Clarke hauled Ipswich level three minutes from time by firing his 16th league goal of the season into the bottom right corner.
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