The Newcastle striker will now miss the Euro 2008 qualifier against Croatia on Wednesday.
England's hopes depend on Saturday's games when Russia's play Israel and Croatia visit Macedonia.
If Russia draw in Israel then England will need to beat Croatia but a loss for Russia would see England needing a point on Wednesday at Wembley.
A loss for Croatia would see England needing to beat them by two goals or more to book a place in next summer's finals.
Manager Steve McClaren is already without forward Wayne Rooney with an ankle injury and Owen's absence would leave him short of options up front.