Raikkonen, a distant 27 points behind Hamilton and only mathematically still in the contest, ruled out any hope of another miracle fightback.
"I'm not thinking about the world championship," said the Finn, back on the front row for the first time since June. "We want to win both championships. It's not going to be easy against the McLarens."
McLaren leads Ferrari by one point in the constructors' championship.
Hamilton, who increased his championship lead over Massa after finishing third in Singapore while the Brazilian failed to score in the night race after a botched pitstop, is bidding to become Formula One's youngest world champion at 23.
Massa now needs a large slice of luck after losing two places in the dying moments of yesterday's final qualifying session when Kovalainen and Alonso lapped faster.
Massa will start alongside BMW-Sauber's Robert Kubica, third in the championship but 20 points behind Hamilton, with the Toyotas of Italian Jarno Trulli and Germany's Timo Glock behind on the fourth row at the Japanese team's home circuit.
Toro Rosso filled the fifth row with Germany's Sebastian Vettel, winner in Italy, and France's Sebastien Bourdais.
Further back, Japan's only grand prix driver Kazuki Nakajima out-qualified his Williams teammate Nico Rosberg to take 14th place for his home debut.
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