A Foreign Ministry statement quoted on state news said Syria was "very surprised" by Brahimi's comments and said it showed "he is fragrantly biased for those who are conspiring against Syria and its people."
The comments come as Russian Deputy Foreign Minister Mikhail Bogdanov is set to travel to Geneva for talks Friday with Brahimi and U.S. Deputy Secretary of State William Burns.
Moscow is lobbying for a new peace initiative by Brahimi based loosely on a pact agreed June 30 by world powers and calling for a transition government.
Russia urged world powers on Thursday to let Syrians decide their own future as it prepared for talks on the 22-month-old crisis.
A firm statement from Moscow said all talk -- particularly that coming from Washington -- on ways to remove Syrian President Bashar al-Assad from power was misguided because the ultimate choice rested with Syrians.
"Only the Syrians themselves can agree on the model of their country's future development," said the Moscow statement.
"Russia's position remains unchanged," it added while urging "all foreign players to redouble their attempts to create conditions conducive for the start of dialogue."
The comments were issued as Russian Deputy Foreign Minister Mikhail Bogdanov went into a closed meeting with his Turkish counterpart Feridun Sinirlioglu.
Syria remains Moscow's last big Middle East ally and has seen its leadership bolstered by Russia's veto of several United Nations attempts to sanction Assad for his bloody crackdown.
But Bogdanov recently told a conference that he felt Assad's days were numbered and that Moscow should be positioning itself for the eventuality of a mixed new opposition team coming to power.