Austin was replaced in the second half at Vitality Stadium by Graziano Pellè after suffering the problem and the Saints boss now expects the January signing to face a spell on the sidelines.
Koeman also saw another striker, Shane Long, go off with a knock after half-time, although he is optimistic that will not be so serious.
“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.”
Koeman admitted it will be a blow to lose one, or even two, forwards as attention now turns to Saturday’s home game against Sunderland.
"Yes, of course, because we like to have everybody available and in ten minutes we lose two front players and that's not so nice,” he said.