The Australian will drop 10 places on the grid after being given his third reprimand of the year for his 'taxi ride' incident in Singapore.
Analysis: why Webber was penalised
The Red Bull driver said his qualifying pace could have been stronger had he not prepared his car to climb through the field on Sunday.
"We had to keep an eye on the race, with the ratios and all those things," said Webber. "You try to have a more balanced view of the weekend as we always knew we would be out of position. I can't qualify on pole 10 places further back than pole.
"You would like to have your cake and eat it and have all the downforce on the car and have super, super top speed but that is not possible.
"We had to take a bit of pace out of the car. I'm pretty happy, I could be two positions further up and be 11th rather than 13th, but it was a pretty tight qualifying.
"We got it right, and the race will be well and truly out of position, but we will try and come back through."
Webber said his car had taken a step forward compared to Friday.
"I think we certainly improved the car in areas we wanted to focus on," he said. "The conditions were a bit different today, we had to keep an eye on that.
"The long runs in practice two won't be too relevant in the race, but we have our ducks lined up and know what we need to work on."