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Sebastian Vettel mastered tricky conditions to claim the 38th pole position of his career in Malaysia.
Rain hit the circuit halfway through Q2, leaving the track wet enough for Intermediate tyres in Q3.
Felipe Massa was second for Ferrari, ahead of team-mate Fernando Alonso in third for the fourth successive race.
Lewis Hamilton was fourth with Mark Webber fifth for Red Bull. Nico Rosberg was sixth, ahead of championship leader Kimi Raikkonen in the Lotus E21.
The wet weather helped McLaren's progress, although they could manage only eighth and tenth in Q3, with Jenson Button edging out Sergio Perez. They were split by the Force India of Adrian Sutil.
The wet weather hindered several drivers in Q2 as Romain Grosjean failed to set a quick enough time and will start eleventh. Paul di Resta suffered a high speed spin on his way to fifteenth.
The most impressive cameo of the day was by Marussia's Jules Bianchi. His time was only 1.6s slower than the quickest time in Q1 and he comfortably beat fellow backmarkers Charles Pic and team-mate Max Chilton.
