The 29-year-old was booed upon being withdrawn in the 68th minute at St Mary's and appeared to direct a two-fingered sign towards the travelling City supporters last month.
The Football Association charged Austin with making "an abusive and/or insulting" gesture and he will now miss Saturday's league trip to Leicester City.
This is not the first time Austin has found himself in disciplinary bother. In 2016 the striker received a three-game fan for violent conduct following a clash with Huddersfield goalkeeper Jonas Lossl.
He may, however, opt to select Shane Long, Danny Ings, Sam Gallagher or Michael Obafemi.
As for Long, he has not netted once in 14 appearances, while Gallagher, has not played a single minute of Premier League football this season.
The only Saints striker who has regularly found the back of the net this campaign is Ings, who has registered an impressive 8 in 16 since his loan move from Liverpool.
Even Austin has not been his usual prolific self and he has contributed just two league goals all season.
The 29-year-old joined Southampton from QPR in 2016 for a reported fee of £4m. Austin has also represented Burnley and Swindon Town.