The 19-year-old suffered the injury in Saturday's 1-0 win at Swansea City, coming off in the 69th minute at Liberty Stadium.
Speaking after his side's 2-1 League Cup victory at Arsenal, Southampton manager Ronald Koeman revealed Ward-Prowse was likely to be sidelined until late in 2014.
"He's not good. He has a stress fracture on his foot," Koeman told BBC Radio.
"Normally he will be out for a long time, maybe between 10-12 weeks. A disappointing situation.
"It's a shame for himself and for the technical staff because now we lose a player for two and half months and we need everybody to be in good shape."
Goals from Dusan Tadic and Nathaniel Clyne helped Southampton to their come-from-behind win at Arsenal on Tuesday.
It marked their fifth straight win in all competitions, and Koeman's side sit second in the Premier League table.
But the Dutchman urged his team to stay focused as they prepare to face QPR on Saturday.
"It's always better to start like this than losing games but we must keep our feet on the ground," Koeman said.
"Saturday will be different. There will be different expectations, and maybe it will be more different to play at home versus QPR than tonight.
"We have to prepare ourselves and we must keep doing what we have since the start of the season."