Saints largely dominated the contest and looked well on their way to three points when Rickie Lambert put them in front after 74 minutes.
However, Scotland's strike from the edge of the area ricocheted past an unfortunate Kelvin Davis five minutes from time to help Ipswich to a scarcely deserved point.
The result means Southampton could be replaced at the summit should West Ham beat Watford at Upton Park tomorrow.
In truth, Saints should have been out of sight against a Tractor Boys side that had conceded the most goals in the division before Lambert finally converted from substitute Steve De Ridder's cross.
Southampton made a decent start and Lambert looked dangerous early on, shooting wide before heading over from Dan Harding's corner.
Davis was equal to Jay Emmanuel-Thomas' long range strike to prevent Ipswich from taking the lead against the run of play.
Adam Lallana thought he had broken the deadlock when he slotted past Alex McCarthy after being played through by Tadanari Lee but the Saints midfielder had been flagged offside before shooting.
In Southampton's next attack, a free-flowing move ended with Dean Hammond squaring for Lallana in the area but he was denied by a marvellous save from McCarthy.
The influential Lallana and Morgan Schneiderlin then combined before the former was once again thwarted by McCarthy.
Guly Do Prado was guilty of missing the target with a free header from Lallana's corner as the hosts laid siege to Ipswich's goal.
It seemed only a matter of time until the deadlock was broken but to their credit, the visitors managed to stifle Southampton's creativity until the interval.
The Tractor Boys had come into the match on the back of a commanding 3-0 victory over Bristol City at the weekend and although they threatened on occasion, they lacked a cutting edge up front.
Michael Chopra should have put them in front at the beginning of the second half, however.
Andy Drury's cross found the striker, who had shaken off his marker but Davis pulled off a fantastic reaction save to keep the scores level.
Davis had shown his worth in Southampton's 1-0 win at Leeds on Saturday and it once again seemed only a moment of brilliance would see his goal breached.
De Ridder was introduced by Saints manager Nigel Adkins for Guly in the 70th minute in an effort to shake things up and the midfielder made an almost immediate impact.
His cross from the right by-line found Lambert at the back post and he drilled past McCarthy in the 74th minute to give Southampton a deserved lead.
Town boss Paul Jewell then made a double substitution, with Scotland and Ryan Stevenson coming on for Drury and Daryl Murphy respectively.
And his changes proved inspired as striker Scotland cut in from the right and his deflected strike from the edge of the area deflected past Davis in the 85th minute to give the visitors a share of the spoils.