A malaise over years of faltering living standards and allegations of corruption from jailed Kremlin critic Alexei Navalny have drained some support, compounded by a tactical voting campaign organised by Navalny's allies.
Kremlin critics, who alleged large-scale vote rigging, said the election was in any case a sham.
United Russia would have fared much worse in a fair contest, given a pre-election crackdown that outlawed Navalny's movement, barred his allies from running and targeted critical media and non-governmental organisations, they said.
Electoral authorities said they had voided any results at voting stations where there had been obvious irregularities and that the overall contest had been fair.
The outcome looks unlikely to change the political landscape, with Putin, who has been in power as president or prime minister since 1999, still dominating ahead of the next presidential election in 2024.
Putin has yet to say whether he will run. He was due to speak on Monday.
The 68-year-old leader remains a popular figure with many Russians who credit him with standing up to the West and restoring national pride.
The near complete results showed the Communist Party finishing in second, followed by the nationalist LDPR party and the Fair Russia party with just over 7 per cent each. All three parties usually back the Kremlin on most key issues.
A new party called "New People", appeared to have squeezed into parliament with just over 5 per cent.
At a celebratory rally at United Russia's headquarters broadcast on state television, Moscow Mayor Sergei Sobyanin, an ally of the Russian leader, shouted: "Putin! Putin! Putin!" to a flag-waving crowd that echoed his chant.
Allies of Navalny, who is serving a jail sentence for parole violations he denies, had encouraged tactical voting against United Russia, a scheme that amounted to supporting the candidate most likely to defeat it in a given electoral district.
In many cases, they had advised people to hold their noses and vote for the Communist Party. Authorities had tried to block the initiative online.
The Central Election Commission was slow to release data from online voting in Moscow, where United Russia traditionally does not fare as well as in other regions amid signs it may have lost some seats in the capital.
Golos, an election watchdog accused by authorities of being a foreign agent, recorded thousands of violations, including threats against observers and ballot stuffing, blatant examples of which circulated on social media. Some individuals were caught on camera depositing bundles of votes in urns.
The Central Election Commission said it had recorded 12 cases of ballot stuffing in eight regions and that the results from those polling stations would be voided.
United Russia held nearly three quarters of the outgoing State Duma's 450 seats. That dominance helped the Kremlin pass constitutional changes last year that allow Putin to run for two more terms as president after 2024, and potentially stay in power until 2036.
Navalny's allies were barred from running in the election after his movement was banned in June as extremist. Other opposition figures allege they were targeted with dirty tricks campaigns.
The Kremlin denies a politically driven crackdown and says individuals are prosecuted for breaking the law. Both it and United Russia denied any role in the registration process for candidates.
"One day we will live in a Russia where it will be possible to vote for good candidates with different political platforms," Navalny ally Leonid Volkov wrote on Telegram messenger before polls closed on Sunday.
One Moscow pensioner who gave his name only as Anatoly said he voted United Russia because he was proud of Putin's efforts to restore what he sees as Russia's rightful great-power status.
"Countries like the United States and Britain more or less respect us now like they respected the Soviet Union in the 1960s and 70s. ... The Anglo-Saxons only understand the language of force," he said.
With official turnout reported to be around only 47 per cent, there were signs of widespread apathy.
"I don't see the point in voting," said one Moscow hairdresser who gave her name as Irina. "It's all been decided for us anyway."