The proceeds from the Nobel Prize medal at the auction in New York on Monday are intended to benefit refugee Ukrainian children.
A previously anonymous bidder secured the award for the medal by telephone.
According to the auction house Heritage Auctions, the proceeds of the auction will go to the aid program for refugee Ukrainian children of the UN children's fund UNICEF.
Muratov is the editor-in-chief of the independent Russian newspaper Novaya Gazeta.
At the end of March, she had to stop appearing after being repeatedly warned by the authorities for her reporting on the Russian invasion of Ukraine.
Muratov was awarded the Nobel Peace Prize last year together with the Filipino journalist Maria Ressa for his services to freedom of expression.
In April, while on a train in Russia, Muratov was attacked with a mixture of oil paint and acetone, which he said caused "terrible" burning in his eyes.
Since 2000, a total of six journalists from Novaya Gazeta have been killed in connection with their work - including investigative reporter Anna Politkovskaya in 2006.