Manager Nigel Adkins' decision to make 11 changes backfired on him in earnest as the Whites secured another top-flight scalp.
The Saints have found life tough since leaving the likes of Leeds behind in the Championship in the summer, accruing just four points from a possible 27.
Even the lure of a quarter-final berth could not lift them as goals from Michael Tonge and El-Hadji Diouf, as well as Luciano Becchio's penalty, saw the home side through.
Tonge opened the scoring in the 35th minute, driving home from 16 yards after Jos Hooiveld failed to fully deal with Luke Varney's cross.
Diouf then appeared to have wrapped things up late on with an easy finish from close range but there was still time for Becchio to convert a last-gasp penalty after Tonge was fouled by Dan Seaborne in the box.
It is not unusual for managers to make changes in this competition - Leeds boss Neil Warnock made four himself - but in view of Southampton's recent struggles, Adkins' choice to rest the entire starting line-up from Sunday's defeat to Tottenham, as well as naming an inexperienced bench, looked somewhat strange.
The tinkering was reflected in Southampton's performance too, with the Saints outplayed by their hosts.
It took until the 70th minute for them to register a shot at goal and it will be Leeds, third-round conquerors of Everton, who enter the hat on Wednesday night for a first quarter-final appearance since 1996 - a year they made the final.
Such an outcome had seemed likely from the moment the teams were named.
With such an array of changes made, Southampton were unlikely to start the better of the two and so it proved, with Leeds and in particular rookie full-back Sam Byram making the early running.
It took until the 15th minute for the home side to fashion a chance of note, though, and when they did, it resulted in what will surely be considered as one of the worst misses in recent memory, with Varney somehow missing from point-blank range.| Leeds United | Team Statistics | Southampton |
| 3 | Goals | 0 |
| 1 | 1st Half Goals | 0 |
| 5 | Shots on Target | 1 |
| 8 | Shots off Target | 1 |
| 1 | Blocked Shots | 2 |
| 8 | Corners | 2 |
| 10 | Fouls | 16 |
| 4 | Offsides | 2 |
| 0 | Yellow Cards | 2 |
| 0 | Red Cards | 0 |
| N/A | Passing Success | N/A |
| N/A | Tackles | N/A |
| N/A | Tackles Success | N/A |
| 41.8 | Possession | 58.2 |
| N/A | Territorial Advantage | N/A |
| 0 | Total Passes | 0 |
| 0 | Total Crosses | 0 |
| 4 | Lost Balls | 2 |
| 2 | Recoveries | 0 |
| 1st Half Poss. | ||
| 2nd Half Poss. | ||
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