Zenit St Petersburg said on their website Kerzhakov, the Russian league's leading scorer with 16 goals, had damaged ligaments in Sunday's 2-2 draw against Spartak Moscow. He could be sidelined for up to two weeks.
Russia coach Dick Advocaat has called up uncapped Rubin Kazan striker Vladimir Dyadyun.
The Russians will also miss first-choice goalkeeper Igor Akinfeyev, out for the rest of the year with a knee injury.
Russia, who lead second-placed Ireland by two points with Armenia and Slovakia three points adrift, host last-placed Andorra in their final qualifier next Tuesday.
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