The 19-year-old suffered the injury during the second half of Saturday's win at Swansea.
"We're very disappointed, but that's football and that can happen," Koeman said. "It's unlucky but OK.
"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."
Up until the injury, Ward-Prowse had played for Southampton in every fixture this season.
Meanwhile, Koeman said that another young English player, Nathaniel Clyne, should be called up by the national side.
The 23-year-old scored Southampton's second in their 2-1 win at Arsenal in the League Cup, with a brilliant 35-yard strike.
"I think he's ready [to play for England]," Koeman said of Clyne, who has played at under-19 and under-21 level.
"He has a lot of experience, he is playing very well from the beginning of the season.
"He scored a great goal. I think his performance was very good and I think it's an option for the national coach and I'm very happy to have Clyney in our team because he brings a lot of experience.
"He brings a lot of spirit and I like to have and play with offensive full-backs. He shows that quality and it's very important for the team."

Pakistan accused India of unprovoked firing in which four civilians died and five others were injured.
India said one woman was killed and three other civilians wounded in firing by Pakistani soldiers.
Pakistan's army also said it shot down an Indian spy drone in Kashmir.
Pakistan summoned the Indian ambassador on Thursday to hear a "strong protest over airspace violation", the AFP news agency quoting a statement issued by the Pakistani foreign ministry said.
The incidents come days after Mr Modi accepted an invitation from Mr Sharif to attend a regional summit in Islamabad next year, signalling a new thaw in a strained relationship. This will be Mr Modi's first visit to Pakistan after he took power last year.
India and Pakistan have often accused each other of unprovoked firing along the disputed border. A ceasefire agreed in 2003 remains in place, but the neighbours often accuse each other of violating it.
Pakistan's military said four civilians, including a 18-year-old girl, had died and five others were wounded when Indian troops fired across the de facto border in Sialkot region on Wednesday morning.
Across the border, Indian border guards said one woman had been killed and three other civilians injured when Pakistani soldiers fired shells which exploded near a border village in Pargwal area on Wednesday.
"It was a blatant, unprovoked cease-fire violation by Pakistan," D Parekh of India's Border Security Force told the Associated Press news agency.
Meanwhile, India's army and air force have denied that any of their drones had been shot down or crashed in Pakistan, reports said.
"An Indian spy drone was shot down by Pakistani troops which intruded into Pakistan along [the de facto border that divides the region] near Bhimber today. The spy drone is used for aerial photography," a statement from the Pakistani military said on Wednesday.
But a spokesperson of the Indian army denied the report.
"Some reports of a drone crash in PoK [Pakistan-controlled Kashmir] are being referred to. No drone or UAV [unmanned aerial vehicle] crash of the Indian Army has taken place," the spokesperson told the Press Trust of India news agency.
An air force spokesperson also denied that any of their drones had been brought down.
Kashmir, claimed by both countries in its entirety, has been a flashpoint for more than 60 years.
Southampton midfielder James Ward-Prowse has been sidelined for 10 weeks with a fractured foot.
[NEXT_CONCEPT]
At least five civilians were killed as India and Pakistan exchanged fire in the disputed Kashmir region, days after a meeting between leaders of the two countries in Russia.