Buoyed by their positive start, Southampton pounced on some static defending by Mustafi and Hector Bellerin to fire his side ahead on 17 minutes.
Danny Welbeck's brace helped Arsenal defy the efforts of desperate Southampton in a 3-2 win at the Emirates Stadium on Sunday.
A precious point was there to be snaffled and, having ruined their first league game under Mark Hughes with a wretched collapse against West Ham last Saturday, that unfamiliar sensation Southampton were experiencing was a surge of optimism.
Despite today's scoreline, Arsenal have struggled in the Premier League this year, with the club now occupying 6th spot in the table.
Charlie Austin restored parity for Southampton in the 73rd minute but Welbeck got the victor eight minutes later from Iwobi's assist.
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Gururaja Poojary picked up silver for India, missing two attempts before a successful last lift that relegated Sri Lanka's Chaturanga Lakmal into third spot.
Southampton were arguably deserving of a point, but Welbeck struck again in the final 10 minutes of the match, to atone for an earlier miss and find the points for his team, despite the game descending into chaos as nerves showed on both sides.
"We came here with a game plan which for the most part worked".
Welbeck was the hero for the hosts, the forward on hand at the back post to nod home Alex Iwobi's deep cross for the victor just moments after he had failed to convert a glaring opportunity inside the six-yard box.
They now lead their quarter-final tie with CSKA Moscow 4-1 after the first-leg.
The goal meant statistics showed Aubameyang has now been involved in seven league goals this term - six goals and one assist - the most of any Arsenal player in their first seven appearances for the club since 1992, the year football was invented.
"Clearly we've got talented players - you've seen that today - we just need that element of determination and ability to affect the opposition when the going gets tough".