The 29-year-old Briton, who won the season-opener in Australia last weekend on Brawn's debut as heirs to departed Honda, will have Toyota's Italian Jarno Trulli alongside on the front row.
Toyota's Timo Glock and fellow-German Nico Rosberg, in a Williams, will fill the second row for what could be a wet and chaotic race that is scheduled to end in the twilight.
As in Melbourne, the grid again had an upside-down look with last year's big guns well down the pecking order.
The pole was the fifth of championship leader Button's roller-coaster Formula One career and the first time he had done it twice in a season. The Briton has already scored more points this year than in the past two.
An hour after qualifying had finished, torrential rain lashed the paddock with flashes of lightning across the darkened skies and thunder crashing around the circuit.
"We've got a lot of thinking overnight to put a plan together if it is wet," said Button, who took the first podium finish of his Formula One career at Sepang when he came third for BAR-Honda in 2004.
"We haven't run this car yet in the wet so it's going to be interesting."Reuse content