"We were racing very hard to keep up with Red Bull," added Hamilton. "We were close but on the knife-edge and I used too much fuel.
scored their biggest points haul from a single race since they returned to the sport in 2010, finishing third and fourth for 27 points in Malaysia. Their previous best was 25 points courtesy of Nico Rosberg's win in China in 2012.
"It's very difficult to make the tyres last too, particularly for me today. I wasn't able to make them last as long as I wanted, and was fuel saving from an early point in the race, which lost me a lot of time.
"I don't know what the situation was with Nico, but I can do a better job looking after tyres."
On lap 51 of the 56 lap race, Rosberg told his team: "I'm so much faster, let me go past."
Brawn replied: "Negative Nico, negative." And later added: "Lewis' pace is what we're asking him to do. He could go a lot faster as well."
However Rosberg stayed close to Hamilton, prompting Brawn to say: "Nico please drop back, there's nothing to gain - I want to bring both cars home please."
Did you know?
Lewis Hamilton finished third in Malaysia for the second successive season. Last year he completed the podium behind Fernando Alonso and Sergio Perez.
When the German, who joined Mercedes in 2010, crossed the line, his engineer said: "Good effort, very well done. You showed what you were able to do today."
Brawn added: "OK thank you Nico, we'll discuss the last thing later, but I'm very pleased with the work this weekend."
Rosberg replied: "Remember this one." Asked by BBC Sport to expand on that comment the German said : "No, it's no question. It was a clear instruction. That's the way it is. It would be the same way if I was in front. I know that.
"It's disappointing for me, I would have liked to have pushed until the end because I was feeling very comfortable. But I'm a Mercedes employee and it's important the team do well.
"We've had a tough time in the past few years, so it's important to get some good results."
Lewis Hamilton makes McLaren pit mistake at Malaysian Grand Prix
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