"Apple paid a 906 million-ruble anti-trust fine," Russia's Federal Anti-Monopoly Service (FAS) said, confirming authorities received the funds.
The case against Apple was initiated by Kaspersky Lab, a Russian cybersecurity firm, which was deemed a national security threat by the United States in March 2022.
Kaspersky said in 2020 that Apple had blocked access to its newly-developed parental control app as the American firm was poised to launch a similar service.
Apple previously told AFP it "respectfully disagreed" with assessment that it had abused its market position. It appealed the decision but Russian courts upheld the ruling.
Apple suspended sales of its products in Russia shortly after the Kremlin deployed troops to Ukraine in February last year.
Russia in 2021 passed legislation requiring all devices with internet access sold in the country to be equipped with approved software produced by Russian companies.
Dubbed the "anti-Apple" law, the controversial bill was introduced in an effort to promote Russia's tech companies but critics said it was an attempt to tighten state control over the internet.
The Kremlin in recent years has isolated Russia from Western tech giants that it believes pose a threat to Moscow's ability to control the distribution of information among Russians.