Rosberg had complained over the radio in the closing stages that he wanted to be allowed past third-placed Hamilton to try and catch the leading Red Bulls.
Team boss Ross Brawn insisted that the duo hold position to save fuel and tyres, but on the podium a subdued Hamilton insisted that Rosberg deserved the place.
Despite his radio angst, Rosberg said at the finish that he understood and accepted Mercedes' stance.
Hamilton said he was proud of the team's handling of the issue, and that the best response would be to work harder to outpace his team-mate.
"We just had a team talk and everyone has been fantastic," Hamilton said.
"The guys did a good job and Nico did an exceptional job. He showed maturity and was in a unique and difficult position.
"But I'm going to work hard - harder - to make sure we're not in that position again.
"It's very difficult. We all work and train hard to win, and to beat the people around us.
"It was an equally difficult situation for me to stay ahead and not let him past, and it was difficult for him to stay behind. For me, I wanted to let him past, but we have standing orders.
"Like I said before, if we didn't have the fuel issue the scenario would have been different today. But hats off to Nico. He was driver of the day for me."
Rosberg reiterated that he saw Mercedes' logic.
"Of course it is tough. I understand their point of view, but I also understood it in the moment," he said.
"Of course I wanted to go for it, and go for the Red Bulls and see what we could do. I don't know how far I would have got and I had to save a bit of fuel again, but nothing unusual."
AUTOSPORT Malaysian GP coverage:
FP1 FP2 FP3 Qualifying Race Gallery Live commentary Official quotes