Jason Euell was Southampton's hero with his first two goals since last April as well as a goalline clearance which came during Ipswich's best spell.
Southampton started brightly with both Marek Saganowski and Andrew Surman seeing shots blocked before Ipswich rallied and strikers Jon Stead and Pablo Counago both shot over.
Southampton thought they had gone in front when Jan-Paul Saeijs headed home a Surman free-kick but it was ruled out for a foul.
However, 60 seconds later a carbon-copy set piece by Surman was nodded in by Euell.
Ipswich came back strongly and after Kelvin Davis could only punch to the edge of the area, David Norris' goalbound lob was headed off the line by Euell.
Ipswich continued to press as half-time approached and Alex Bruce saw his shot deflect off Chris Perry and onto the crossbar before Stead's overhead kick flashed inches wide.
Ipswich boss Jim Magilton made a double substitution at the break, sending on Kevin Lisbie and Jon Walters but it was Southampton who continued to threaten.
Saganowski drew a save out of Richard Wright as did David McGoldrick, who also sent a curling effort inches past the far post.
Ipswich had two great opportunities to draw level but Pim Balkestein headed over from close range and Lisbie shot narrowly wide on the turn.
Saints had always looked dangerous on the break and they sealed the points with two late goals as first Euell latched onto a weak back header from Balkestein and although Richard Wright saved his initial shot he lashed home the rebound.
Substitute Matthew Paterson put the gloss on the victory a minute after coming on when he robbed Norris and ran on to fire into the corner.