The vote comes in the wake of an unprecedented crackdown on the opposition this year, with Russian authorities jailing Putin's best-known domestic foe Alexei Navalny and banning his organisations as "extremist".
In the lead-up to this weekend's vote, all of his top allies were arrested or had fled the country, with anyone associated with his groups kept from running in the parliamentary and local polls scheduled to close at 8:00 pm Sunday.
"These essentially aren't elections. People in effect have no choice," 43-year-old businessman Vladimir Zakharov told AFP in Russia's second city Saint Petersburg.
The elections were also marred by claims of censorship and rampant ballot stuffing.
As voting kicked off Friday, Apple and Google caused an uproar among Russia's opposition after they removed Navalny's "Smart Voting" app, which showed supporters which candidate they should back to unseat Kremlin-aligned politicians.
Sources familiar with Google and Apple's decision told AFP the move was taken under pressure from Russian authorities, including threats to arrest the tech giants' local staff.
By late Friday, the popular Telegram messenger had also removed Navalny's "Smart Voting" bot, and by the early hours of Sunday Google Docs and YouTube videos containing the lists of the recommended candidates had also been blocked.
Navalny's team said that Google, which did not immediately respond to a request for comment from AFP, had complied with demands made by Russia's media regulator Roskomnadzor.
They also swiftly made new Google Docs and YouTube videos with the lists.
"How quickly will Roskomnadzor write another request and YouTube will fulfil it? Let's see," Navalny's banned Anti-Corruption Foundation tweeted.
Russian social media meanwhile was inundated with reports of ballot stuffing and military servicemen patrolling polling stations.
Critics also pointed to online voting, new limits on independent election observers and the polls being spread over three days as presenting opportunities for mass voting fraud.
As of Saturday afternoon, the independent Golos election monitor -- which authorities branded a "foreign agent" ahead of the polls -- had tracked more than 2,750 reports of voting violations.
Elections chief Ella Pamfilova said Saturday her commission had received 137 reports of voting "coercion".
Going into the lower house State Duma vote, Putin's United Russia party was polling at historical lows.
Recent surveys by state-run pollster VTsIOM showed fewer than 30 percent of Russians planning to vote for the party, down at least 10 percentage points in the weeks ahead of the last parliamentary election in 2016.
While 68-year-old Putin remains popular, United Russia has seen its support drop as living standards decline following years of economic stagnation.
But the ruling party is widely expected to retain its two-thirds majority in the lower house, allowing it to push through legislative changes without resistance.
In addition to United Russia, 13 more parties are running in the elections. They, however, are widely seen as token opposition doing the Kremlin's bidding.
On Saturday, Navalny ally Leonid Volkov said "Putin was celebrating a huge victory" after tech giants "caved under the Kremlin's blackmail" but still called on supporters to try to turn the Russian leader's jubilant mood into "mourning".
"In our battle between David and Goliath, we definitely still have the opportunity to launch the stone," he wrote on Telegram.
