Vettel put Red Bull in the coveted No. 1 position for the second time in the first two races of the F1 season by navigating the 3.44-mile Sepang Circuit course in 1 minute 49.674 seconds.
Ferrari took the next two starting positions for Sunday's race. Kimi Raikkonen, who won last weekend's season opener in Australia, was bumped down to seventh position when he was penalized for impeding.
Rain slowed down Saturday's qualifying run.