The journalist’s arrest last week was widely seen as punishment for his investigative work and sparked an unprecedented campaign of solidarity in Russian society.
On Tuesday, Interior Minister Vladimir Kolokoltsev said he had requested Putin dismiss the officers after lifting the charges against Golunov on the basis of a lack of evidence.
On Thursday, Putin signed a decree to dismiss the police chief for western Moscow, Major General Andrei Puchkov, and the head of the Moscow police department for narcotics control, Major General Yury Devyatkin.
Golunov is a reporter for Meduza news site, which is based in EU member Latvia. He walked free from a Moscow police building on Tuesday evening after his house arrest was lifted.
Moscow police had charged him with attempted drug dealing, saying that officers found him in possession of drugs including cocaine.
But as the details of the case attracted public outrage, they later admitted that they had posted photographs of drugs paraphernalia that were not taken in his flat.
Golunov’s supporters, including many influential journalists, mounted a public campaign in his defence, holding protests outside Moscow police headquarters.
The case has prompted wide-reaching questions about how Russian police operate, with Golunov’s supporters and lawyers saying that police planted drugs on him.
Kolokoltsev said the police who worked on the case have been suspended pending an investigation.
On Wednesday, a few thousand protesters took to the streets of Moscow for an unsanctioned march calling for broad reform of the law enforcement and justice systems.
Police violently broke up the march and arrested more than 500 people, according to OVD INFO, a monitor that tracks detentions.