Polls opened across the vast country on Friday after a year that saw a sweeping crackdown on President Vladimir Putin's opponents, with Russians given the option of voting online.
State media showed Putin casting his ballot online from self-isolation, several days into quarantine after coming into contact with Covid-19.
As voting began, the opposition said a "Smart Voting" app advising supporters on how to vote out Kremlin allies had been removed from the app stores of both Apple and Google.
"They caved in to the Kremlin's blackmail," Leonid Volkov, an exiled aide to Navalny, said on Telegram, after Moscow accused the US tech giants of election interference and demanded they remove the app.
Navalny ally Ivan Zhdanov accused the companies of a "shameful act of political censorship", posting a screenshot on Twitter of an email from Apple saying the app was removed because Navalny's organisation has been declared "extremist".
He said the US companies were making a "huge mistake".
Sources familiar with Google and Apple's decision said the move was taken under pressure from Russian authorities, including threats to arrest local staff of the tech giant.
One source said Apple employees faced mounting "bullying tactics and threats to arrest" at the start of the vote, while another noted Google had acted under "extraordinary duress".
The Kremlin welcomed the move, saying the tech giants had conformed with "the letter and spirit" of Russian law.
The app instructed Russians on how to vote strategically to try to defeat politicians from Putin's United Russia party, after candidates critical of the Kremlin were largely barred from running in the vote.
In power for two decades, Putin's tenure has seen tightening controls over the Russian segment of the internet. (AFP)