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Alonso, who narrowly beat Schumacher in Bahrain, was eighth in qualifying with a time of 1:35.747.
"It was obviously a very disappointing qualifying session for me," Alonso said. "Fisico (Fisichella) showed what the car can do at this circuit and I should have been up there as well."
Renault's Alonso claimed pole here in 2005 with a time of 1:35.090.
Alonso likes it here. He won in Malaysia last year _ the beginning of a three-race winning streak that he used as a springboard for the Formula One drivers' title.
Kimi Raikkonen, the 2003 winner in Malaysia, fared better than last week when his McLaren-Mercedes broke a rear suspension in qualifying, forcing him to start last in the race. He is seventh in 1:34.983.
Massa ended up 16th in qualifying and will start in the last row, probably with a full fuel tank as he did not even go out in the second session Saturday.