Alonso, who started the 2003 race from pole position, clocked a lap of one minute 32.582 seconds -- the fastest yet at the Sepang circuit.
His time was 0.090 quicker than Italian Jarno Trulli, who placed his Toyota on the overnight front row before Sunday's final qualifying session, and nearly half a second faster than last year's pole time.
Championship leader Giancarlo Fisichella, who gave Renault a season-opening victory in Australia on March 6, was third quickest ahead of McLaren's Kimi Raikkonen.
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The speed of the Toyotas, both out of the points in Australia, was the main surprise of a session that also had champions Ferrari well down the timesheets.
Germany's Ralf Schumacher was fifth fastest for Toyota while his older brother, Ferrari's seven times world champion Michael, was 12th.
Michael Schumacher, chasing his first points of the new campaign after failing to finish in Melbourne, was a hefty 1.490 seconds slower than Alonso.
The German, who will try out Ferrari's new car for the first time next week and could race it at the next round in Bahrain after starting the season with a modified version of last year's F2004, was two places ahead of team mate Rubens Barrichello.
Briton Anthony Davidson, replacing Takuma Sato at Honda-powered BAR after the Japanese was laid low by a fever, qualified 15th.
Compatriot and team mate Jenson Button, who had the first podium of his Formula One career in Malaysia last year when he finished third, was ninth.
Brazilian Felipe Massa kept Sauber team mate and 1997 world champion Jacques Villeneuve behind him, qualifying 13th to the Canadian's 16th place.
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