It was a third draw in a row for the Gunners and their pursuit of the title is no longer in their own hands.
Manchester City are now five points behind but with two games in hand - and host the Gunners at Etihad Stadium next Wednesday.
Saints led after just 28 seconds, when Carlos Alcaraz capitalised on an Aaron Ramsdale error to score.
Arsenal have now conceded the two fastest goals at home in the Premier League this season, the other being Philip Billing's strike after 9.11 seconds for Bournemouth.
Theo Walcott doubled the Southampton lead against his former club, before Gabriel Martinelli pulled one back for the league leaders.
Duje Caleta-Car restored the Southampton two-goal advantage and appeared to seal the three points - only for Martin Odegaard and Bukayo Saka to score in the 88th and 90th minutes to earn a draw.
It follows draws away to Liverpool and West Ham United for Mikel Arteta's side in their previous two games.
Southampton remain bottom of the table and three points from safety, having now failed to win in seven league games.
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