The Manchester United striker was substituted after the first half of a goalless draw against Reading following a clash with Michael Duberry.
The post-game medical scan showed that Rooney had received a hairline fracture to his foot and will miss several weeks of training and games.
But Alex Ferguson, Rooney's manager, downsized the importance of the injury as he said, "It was a painful blow and Wayne could not really stand on his foot, but I do not think it is as serious an injury as when he broke his metatarsal."
"The foot did start to swell and it was not worth starting him in the second half," UEFA Web site said citing Ferguson.
England, which has given unexpectedly poor performances since the beginning of the qualifiers, returned home in June from Tallinn after a convincing 3-0 victory over Estonia. The victory was largely down to the experience of Michael Owen and David Beckham, who were missing from previous qualifiers.
Speaking earlier about Russia's chances of qualifying for the championship in Austria and Switzerland next year, Russia's Dutch coach Guus Hiddink, 60, who signed a two-year contract worth 4 million euros last year to head the Russian team, said everything would be decided in the fall when Russia meets England.
Hiddink said that with England's victory the fight within the group, which he dubbed as the "group of death," reached a climax and only the last games in November will show, who will get the tickets to the 2008 Euro finals.