The German, in a world of his own in the opening race in Australia as he launched his bid for an unprecedented seventh championship, blasted around the steamy Sepang circuit quicker than ever.
He led the first of two 45 minute sessions with a fastest time of one minute 33.391 seconds in brilliant sunshine.
Schumacher then stayed top in the second with a time of 1:33.526, 0.037 faster than the Williams of Colombian Juan Pablo Montoya.
McLaren's Kimi Raikkonen, fastest on Friday, failed to set a time in the first session but was seventh quickest in the final run before the afternoon's controversial and soon to be modified qualifying marathon.
While Ferrari remained in front, Schumacher's rivals could take heart that the gap between them and the red cars had narrowed.
Renault's Fernando Alonso, the Spaniard who started last year's race as the youngest grand prix driver to secure pole position, was second quickest in the first session with a lap 0.784 of a second slower than Schumacher.
By the final practice session, watched by a sparse crowd on a general election weekend in Malaysia, the top nine were within that margin.
Schumacher's younger brother Ralf was third quickest in a Williams, 0.447 slower than the Ferrari, with Renault's Jarno Trulli fourth and Brazilian Rubens Barrichello fifth in the second Ferrari.
Briton Jenson Button, in a BAR, last year's race winner Raikkonen and McLaren team mate David Coulthard followed with Ferrari's Bridgestone tyre supplier facing a strong challenge from Michelin in rising temperatures.
The French manufacturer had eight cars in the top 10.
Malaysia, with air temperatures of around 34 degrees Celsius on Saturday morning, has been one of the hottest and most demanding races on the calendar although next month's inaugural Bahrain Grand Prix could challenge that.
Sunday's race is also seen as a key test for Ferrari's rivals after the champions' dominance in Melbourne.
Another Ferrari victory could signal the start of another record-breaking year for Schumacher.
