The striker, who only joined the Saints in January, was replaced by Graziano Pelle on the hour mark, and needed to be helped off the pitch by the club's medical team.
Ten minutes later, his strike partner Shane Long also left the field with an injury, but the Dutchman says that news on the Republic of Ireland marksman is not as bad as Austin's.
"For sure Charlie is a hamstring injury, [that’s] what I heard from the doctor,” Koeman is quoted as saying by Southampton’s official website.
“Shane was a kick on his knee and I think that's not so bad, but I think Charlie will be out for several weeks.”
The ex-QPR man has a history of lengthy injuries, and suffice to say that the news did not go down well with Southampton supporters.
Charlie Austin was barely match fit and now he's injured and out for several weeks. Sound.— Emma (@_EmBen) March 1, 2016
Gutted to see @chazaustin9 come off.. Hopefully back asap⚽️⚽️— Bianca Austin (@Biancajayde1990) March 1, 2016
Gutted to see @chazaustin9 limp off! Hope he's not out for to long. Chin up mate!— Gary crame (@crammy9) March 1, 2016
Austin has netted one Premier League goal following his move to the South Coast.