Southampton looked to be heading for a fifth defeat in their opening six matches until Czech Republic youngster Pekhart struck with his first goal in English football 22 minutes from time.
Pekhart, on loan from Tottenham, lashed the ball into the roof of the net after David McGoldrick's shot had bounced off his heel, 15 minutes after being brought on by a desperate Poortvliet.
The match was watched by a record low league gate of just 14,961 at the St Mary's Stadium but Southampton gave those fans who did turn up a dream start when Andrew Surman opened the scoring after just 12 minutes.
England Under-21 star Surman picked up the ball on the left wing before cutting on to his right foot and slotting a 25-yard shot into the bottom left-hand corner of the Ipswich goal.
Town struck back within eight minutes when midfielder Owen Garvan grabbed his first goal of the season after taking advantage of some haphazard defending from the home side.
David Norris' shot had been well-saved by goalkeeper Kelvin Davis but Saints failed to get the ball clear, allowing the grateful Garvan to pick out the top corner of the net from six yards out.
Saints had Davis to thank for going in level at half-time after a brilliant double save in the 25th minute.
Jon Stead looked certain to score for the second match in a row before Davis spread himself superbly to keep out the former Sunderland star's close-range effort.
Davis was called into action again just 30 seconds later when he acrobatically turned Norris' header over his crossbar.
Ipswich got the goal they fully deserved five minutes after the restart when the diminutive Alan Quinn rose to head home new signing Moritz Volz's cross.
The visitors thought they had secured their second away success of the season before Pekhart's heroics, but could have been further in front but for some wasteful finishing by substitute Pablo Counago, who missed two good chances.