"It cost us three points and potentially the championship and we are perfectly conscious about that," team boss Toto Wolff said after Hamilton slowed on the final lap to let team mate Valtteri Bottas take third place as part of an earlier agreement.
"Nevertheless this is how the drivers and team operate," added the Austrian, whose team have won the past three drivers' and constructors' championships.
"We stick to what we say and if the consequences are as much as losing the championship, we take it.
"But long term we will be winning much more races and championships with that approach than doing it the other way around."
Bottas had agreed to let the faster Hamilton through to chase the leading Ferraris, on the understanding that the positions would be reversed again if unsuccessful.
The Briton duly kept his word, even if others might not have done with so much at stake, and fell 14 points behind Ferrari's championship leader and race winner Sebastian Vettel.
Formula One history has countless examples of teams forcing drivers to obey orders but usually with one dominant player benefiting.
Ferrari, during the Michael Schumacher era of dominance, were famed for favouring the German at the expense of his team mates, even when they were deservedly leading with no other rivals to worry about.
They have continued with that approach in recent years, with Kimi Raikkonen clearly unhappy at being kept behind his slower team mate on Sunday.
It is rare indeed for a star driver in a tight battle for the championship, and whose team mate is behind in the standings, to give up points that could make or break his chances without affecting the constructor's tally.
Wolff said he would be the first to "shoot myself in the knee" if the championship ultimately hinged on those three points but he added that Mercedes had a bigger picture in mind.
"We drive in circles because we hope that it promotes our brand and makes us sell cars and it’s a very long-term project," he said.
"And we’ve seen the backlash of decisions that were ruthless and cold-blooded and the effect it had on the brand. Now you say ‘Screw it, it still won them the championship. Who cares? They are down in the history books’.
"But I don’t think this is the right spin. If I come back to what I think the purpose of us being here is, it is doing the right things and winning in the right way. And sometimes doing it the right way and standing by your values is tough.
"It was today, believe me."
(Editing by Clare Fallon)
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