McClaren said: "Owen won't be fit for Wednesday. It was a strange one, it was his standing foot and he pulled his thigh.
"It's unfortunate but I do believe we need to win on Wednesday to qualify.
"We seem to be plagued with injuries at the moment. We'll be going into our biggest game for some while without our two first-choice centre-forwards and two first-choice centre-backs.
"But I believe there's enough in that dressing room to get through this game.
"We've got Crouch's height and our midfielders are capable of scoring goals."
Liverpool's 6ft 7in striker Crouch scored his 13th goal in 23 appearances and will now have to lead the attack against Croatia at Wembley - a game that could determine McClaren's future.
David Beckham played an hour against Austria and is likely to win his 99th cap on Wednesday.
McClaren remains confident about Israel's chances of getting a result against Russia today.
He said: "I'm as confident as anyone can be. Believe me, the players won't see it as a meaningless game for Israel.
"There's a lot riding on it for them - their home record and pride plus they'll be the focus of attention."