Toyota’s Jarno Trulli impressed during Saturday and will be second on the grid ahead of team-mate Timo Glock.
Ferrari’s miserable season continued with the shock early departure of Felipe Massa, who finished in 16th spot in the first qualifying session.
McLaren’s Lewis Hamilton made it one stage further and will start 13th.
Clouds hovered over the Sepang circuit throughout Saturday’s sessions, with the track temperature reaching a steamy 44C (111F) but the rain many thought would fall never arrived.
England’s Button set a time of one minute 35.181 seconds to secure his second successive pole position and fifth in his career to finish almost a tenth of a second ahead of Italy’s Trulli.
Button claimed to be less than happy with his car after Friday’s practice sessions but the 29-year-old was satisfied with adjustments made overnight.
"I was really struggling with the balance of the car. I had a lot of rear locking and instability, and when I have that it’s not my forte really because I find it difficult to drive it around," he said.
"So we changed it around overnight and it’s improved it a lot and I feel very comfortable in the car, so it makes it exciting for tomorrow."
Many predicted Brawn would continue their domination following their phenomenal one-two placing in Melbourne last week.
But they did not have it all their own way with Rubens Barrichello back on the fifth row following his five-place grid penalty for using a new gearbox on Friday.
Glock recorded only the fifth best time in final qualifying but will be third on the grid in his Toyota as a result of penalties handed out to Sebastian Vettel and Barrichello.
Hamilton, with much on his mind after being stripped of a third place in Australia for misleading stewards in an inquiry, as well as being fined for breaching the pit lane speed limit on Friday, will start in 12th after failing to reach the final stage of qualifying.
Ferrari opted for Massa to complete just four laps but the plan back-fired with several late quick times to leave the Brazilian in 16th spot in the first qualifying session.
Massa told BBC Sport: "I needed to do the perfect lap but I didn’t do it. It was a big surprise not to make the top 15 – it was a bit of a mistake."