"He got injured last time and he got a recurrence of that," Wenger said after the game.
"We'll see. I don't know," Wenger said when asked if he was fit for the trip to St Mary's Stadium.
Xhaka, who joined Arsenal before the start of the season, has scored four goals in 41 appearances for the club in all competitions.
"He has improved from the start to now," Wenger told the BBC. "He is slowly getting stature in the middle of the park."
Sixth-placed Arsenal beat Southampton 5-0 in the FA Cup in January but have recorded one league win in their last six visits to St Mary's.
(Reporting by Aditi Prakash in Bengaluru)
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