In a third-round replay between the third-placed teams in the Premier League and Championship respectively, quality ultimately showed at Portman Road as Long's goal proved the difference.
Ronald Koeman's side, which saw five changes from Sunday's win at Manchester United, were made to sweat at points in the game, but the in-form visitors rarely looked like suffering an upset.
Ipswich had the better of the early exchanges, Long pouncing on a loose ball to give the Premier League side the lead 19 minutes into a tie that will not live long in the memory.
A positive half for Koeman was dampened somewhat by Victor Wanyama's injury-enforced withdrawal, as Southampton proceeded to labour after the break.
However, Southampton did enough to keep Ipswich contained as Long - who was cup-tied during former club Hull City's run to the final last season - made the most of a rare start ahead of Graziano Pelle to settle the tie and set up a fourth-round clash against Crystal Palace.
With Ipswich starting brightly, Stephen Hunt had the ball in the net after five minutes, only for it to be adjudged offside.
As Southampton grew into the game, Long made the most of the visitors' first clear-cut chance with a clinical finish from inside the area.
Luke Chambers' tackle on Harrison Reed pushed the ball into Long's path and the Irishman made no mistake – netting his first goal since November.
Long's predatory strike added to Southampton's momentum, with James Ward-Prowse's long-range strike next to threaten the goal of former Southampton goalkeeper Bartosz Bialkowski.
After Dusan Tadic's strike was blocked by Christophe Berra, Ward-Prowse again let fly with a wayward effort before David McGoldrick spurning a rare Ipswich foray forward by firing high and wide from a narrow angle before the interval.
With Southampton struggling to kill the game off, Darren Ambrose - who was on target when the first game ended 1-1 - had a header on target for Ipswich as the hosts sought to crank up the pressure.
Tyrone Mings supplied the cross for Ambrose and the introduction of the former - a former Saints prospect - livened up proceedings.
However, Mick McCarthy's side were hampered by the withdrawal of McGoldrick minutes after the forward appeared to injure himself in a challenge on Jose Fonte.
Ipswich struggled in a lacklustre final 20 minutes as Southampton were able to see out the result and book a home clash with Palace in the fourth round.
However, with Wanyama potentially joining the likes of Morgan Schneiderlin and Toby Alderweireld on the treatment table, Koeman will hope Wednesday's win does not come at too much of a cost.
