Midfielder Denisov, who this month was made Russia captain by Capello, has been demoted to Zenit's reserve team after he refused to play for the club and issued an ultimatum to renegotiate his contract.
Kerzhakov was also demoted for "improper behaviour", Zenit said.
Former national team skipper Andrei Arshavin was left out by Capello because the Arsenal forward has seen little action for his London club this season.
Italian Capello, who replaced Dick Advocaat last month following Russia's poor showing at Euro 2012, also dropped experienced strikers Roman Pavlyuchenko and Pavel Pogrebnyak, preferring to call up 22-year-old newcomer Maxim Grigoryev and Artem Dzyuba.
Dzyuba, 24, has only one international cap after starting for Russia in a friendly against Greece last November.
Former Chelsea winger Yuri Zhirkov, who joined wealthy Anzhi Makhachkala last year, was recalled after missing Russia's first two qualifiers against Northern Ireland and Israel with injury.
The squad will be trimmed to 23 players by Capello next week, the Russian FA said on its website.
The Russians have made a flying start in their World Cup qualifying campaign under Capello, winning both matches.
They face joint Group F rivals Portugal in Moscow on Oct. 12 before hosting fifth-placed Azerbaijan four days later.