Opposition parties criticised Putin, alleging that numerous instances of pressure on voters, a one-sided campaign and systematic electoral fraud had compromised the result.
Al Jazeera's Laurence Lee, reporting from Moscow on Sunday, said there were suggestions that people were being forced to go out and vote.
"It's a referendum on Putin, and they've said that. But in order to legitimise that it needs a high turn out - it needs to have a popular mandate.
"Some people have suggested that they are actually forcing people to go out and vote to get that high turnout," he said.
The last polling stations closed at 9pm (1800 GMT), but the vote takes place across 11 time zones.
About 109 million voters can cast their ballots in the fifth election since the collapse of the Soviet Union in 1991.
A former officer with the KGB, the Soviet Union's intelligence agency, Putin has been president since 2000, and is barred from running for a third consecutive term by the constitution.
However, Putin announced on October 1 that he would head United Russia's list for the elections, guaranteeing him a place in the Duma - Russia's lower house of parliament.
The party usually labels itself as a centrist party and was founded in April 2001. It has been making gains in recent federal and local elections due to the popularity of Putin, although he is a non-member.
Putin has cast the election as a referendum on his rule, saying that a vote for United Russia would safeguard the country's oil-driven economic boom and stability.
"The result of the parliamentary elections will, without a doubt, set the tone for the elections for a new president," Putin said in a televised address aired for a second time on Friday.
In his final pitch to voters, Putin urged them to turn out, claiming that a vote for his opponents could return the country to the "humiliation, dependency and disintegration" of the early post-Soviet years.
As required by law, a campaign blackout started at midnight on Friday, although United Russia posters remained in the capital, Moscow, while those of the 10 other parties were less visible.
Sergei Mitrokhin, deputy chairman of the Yabloko party, told radio Ekho Moskvy that he had complained to the central election commission about Putin's speech."This was a flagrant violation of the legislation, an abuse of office in the interests of one party," he said.
The opposition has accused the Kremlin of suppressing debate during the campaign by dominating coverage on state-run TV, confiscating their election leaflets and arresting members.
Stanislav Babin, running for the Union of Right-Wing Forces (SPS) party in the Black Sea Krasnodar region, said that a dozen police officers had tried to break into the party's local branch on Saturday.
"This is official pressure on the SPS. Eighty thousand copies of our election leaflets have been confiscated for being 'extremist'."
Garry Kasparov, a critic of the Kremlin, has dismissed the elections as a "farce" and warned that Putin is leading the country towards dictatorship.
After being detained for five days this week for taking part in an unauthorised protest against Putin, Kasparov accused the president of resorting to repression to cement his party's dominance.
"Fear is the only chance this regime has to survive," Kasparov said.
Election monitors say they are concerned by allegations that voters are being pressured by the authorities to vote at their workplaces, under the supervision of their bosses.
Opinion polls showed that the Communist party was the only party other than United Russia that was assured of exceeding the seven per cent threshold required to qualify for seats in the new Duma.
About 450,000 police officers were on duty on Sunday, and 95,000 polling stations were set up across Russia's 11 time zones.