The three-day vote that ended on Sunday followed an unprecedented crackdown on critics of President Vladimir Putin and came with pre-election polls showing United Russia's popularity at a historic low.
But the party still claimed a two-thirds majority in the lower house State Duma, with United Russia's Andrei Turchak saying it was a "convincing and clear victory".
He told reporters the party had taken 120 seats from the party list and 195 single-mandate seats -- a total of 315 seats from 450.
It was a drop from the 334 seats United Russia held before the election, but still enough for the party to enact major legislation including changes to the constitution.
With 85 percent of votes counted by 0700 GMT on Monday, United Russia was ahead with 49.76 percent of the vote followed by the Communist Party with 19.61 percent.
Even predictions by state-run pollsters had suggested United Russia winning only around 30 percent.
Allies of jailed Kremlin critic Alexei Navalny, Russia's leading opposition figure, called the results outlandish.
"This is truly unbelievable. I remember the feeling in 2011, when they stole the election. The same is happening right now," said Navalny's spokeswoman Kira Yarmysh.
Claims of widespread fraud in 2011 sparked huge protests led by Navalny, who was arrested in January and jailed following a poisoning he blamed on the Kremlin.
His allies said the vote was being falsified on a massive scale, pointing especially to repeated delays in releasing the results of electronic voting in opposition-friendly Moscow.
Navalny's organisations were banned as "extremist" ahead of the election and his top allies were arrested or fled and anyone associated with his groups were kept from running.
Navalny's team had called for opposition supporters to back other candidates who could potentially defeat United Russia, most of them from the Communist Party, and results indicated the "Smart Voting" campaign may have had some impact.
United Russia's share of the vote was down from 54.2 percent in the last parliamentary election in 2016, while the Communists saw their support grow from 13.3 percent.
Three other parties appeared to have met the five percent threshold needed to enter parliament -- the nationalist LDPR, the recently formed "New People" party, and "A Just Russia", all with less than 10 percent.
Navalny's top ally Leonid Volkov said the tactical voting project had "rattled" Russia's political elite.
"We forced them to either admit defeat or to falsify, in front of everyone, absolutely brazenly, without any shame. To admit moral bankruptcy," Volkov said during a post-election live stream on YouTube.
Authorities took drastic measures to deter the "Smart Voting" campaign, which provided lists of candidates with the best hope of denying Kremlin-aligned politicians a seat.
The campaign's website was shut down and Apple and Google removed the Smart Voting app from their stores, reportedly under threats to arrest their local staff.
The popular Telegram messenger also removed Navalny's Smart Voting bot, and Google Docs and YouTube videos containing the lists of recommended candidates were blocked.
Turnout was at 45 percent, according to the latest figures released by the election commission on Sunday.
Critics had argued that online voting, new limits on election observers and the polls being spread over three days -- a move officials said was to reduce coronavirus risks -- all presented opportunities for fraud.
As of Sunday evening, independent election monitor Golos -- which authorities branded a "foreign agent" ahead of the polls -- had tracked over 4,900 reports of voting violations.
United Russia has seen its popularity drop as living standards decline following years of economic stagnation.
But Putin, 68 and in power for two decades, remains popular, and some voters said they backed the party out of trust in him.
"We just don't see anyone else we can trust in the current political landscape," Anna Kartashova, a 50-year-old pharmaceutical company manager in Moscow, said as she voted in Moscow.
