Many, including Arsene Wenger, had expected Saints to implode after a summer in which they lost manager Mauricio Pochettino and a host of key players. However, Ronald Koeman’s side continue to confound the doubters and won a fifth successive match in all competitions at a sold-out Emirates, where 5,000 visiting fans roared Southampton on against the much-changed Gunners.
Wenger called Saints “miracle workers” in the build-up to the third-round tie, which looked likely a particularly tall order when Alexis Sanchez fired home a wonderful 25-yard free-kick with just 14 minutes on the clock.
The visitors did not wilt, though and Sadio Mane, belatedly making his debut after work permit problems, quickly earned a penalty off Tomas Rosicky, which fellow summer signing Dusan Tadic slotted home.
Graziano Pelle clipped the woodwork as Southampton continued to boss Arsenal’s inexperienced defence, which could only watch on helplessly as Clyne thundered home a wonderful goal from 30 yards.
Debutant David Ospina could not get a hand to the fierce drive, although did well to keep his side in the game with a fine save to thwart Steven Davis and then Tadic.
Saints had to defend resolutely as the match came to a close but held out for a first win against Arsenal since 2002, continuing Wenger’s wait to get his hands on the one domestic trophy to have eluded him.
The Frenchman made 10 changes, including giving injury-plagued Abou Diaby his first start in 18 months.
The only survivor from the league win at Aston Villa was Calum Chambers, facing the club he left in the summer as part of a back four with just 54 Arsenal appearances between them — the majority by Francis Coquelin, playing out-of-position at left-back.
That inexperience showed on the night and Southampton take full advantage.
ARSENAL: Ospina, Hayden, Coquelin, Bellerín (Akpom 86), Chambers, Rosicky, Abou Diaby (Cazorla 67), Sanchez, Wilshere, Campbell, (Oxlade-Chamberlain 71), Podolski.
SOUTHAMPTON: Forster, Targett (Bertrand 85), Fonte, Clyne, Gardos, Davis, Schneiderlin, Wanyama, Pelle, Tadic, Mane (Long 72).
Referee: Keith Stroud.