The 19-year-old was stretchered off in the second half of the 1-0 win away at Swansea City on Saturday.
Saints boss Ronald Koeman rested him for the Capital One Cup third-round victory over Arsenal in the hope that he could be fit to feature against Queens Park Rangers in the Premier League this weekend.
However, scans have since shown that the damage to Ward-Prowse's foot was more substantial than first thought, and the teenager is unlikely to feature again for Southampton until at least December.
"We're very disappointed about that, but that's football and that can happen," Koeman told reporters. "It's unlucky but okay.
"The boy has to keep going and it's difficult because he had a great start to the season, but it's part of the football and he will come back."
Ward-Prowse will also be forced to sit out England Under-21s' European Championship playoff with Croatia.