On a wet afternoon at the Sepang International Circuit, Hulkenberg's VJM07-04 clocked 2:01.712 in Q3 while Perez clocked 2:02.511 in Q2.
Hulkenberg expressed happiness at the result of the qualifying race of the second leg of the F1 Championships.
"It was pretty challenging with the weather conditions today. There was so much rain, standing water and spray. Visibility was an issue and it was hard to see your braking points. It's tricky to drive these engines with lots of torque in these conditions and you need to be really smooth with the throttle out of the slow corners, but I enjoyed the challenge," he said.
Perez said he faced problems in his car while driving on the wet track.
""The conditions out there were very difficult and they kept changing with every lap, especially during Q2. I had a better feeling on the intermediate tyres and when I changed to the full wets I struggled to keep the temperature in them, which made it hard to put together a good lap. Tomorrow we will need to try and recover from P14, but we have to see what the weather will do.