By Monday morning, early results indicated a huge slide in support for the once powerful communists.
The Communist Party's leader denounced the polls as a farce riddled with cheating after an exit poll and the first official results from Russia's far east showed the pro-Kremlin United Russia winning easily twice as many votes as the communists.
The fourth election since the Soviet Union collapsed looks set to hand the highly popular Putin greater powers to drive economic reform, crack down on corruption, boost his bureaucracy and rein in the business elite in a country craving stability.
But critics say a pro-Putin majority in the State Duma lower house will help Kremlin ex-KGB hardliners who want to revive authoritarian rule. Opposition parties accuse them of using state resources and media controls to promote United Russia.
"It looks like we are in for a dose of concentrated Putinism for the next four years," said Roland Nash, head of research at the Renaissance Capital investment bank.
Early results released by the electoral commission said United Russia had scored 36.4%, slightly more than the 34% predicted by an exit poll.
The results put the communists, who form the main opposition to Putin, on only 13% - way down from the 24% they garnered in the 1999 election.
"This is a shameful farce which has nothing in common with the country's interests," Communist Party chief Gennady Zyuganov told a news conference.
Communist leader Zyuganov calls the election a 'farce'
"You are all participants here in a revolting spectacle which for some reason is called an election."
Ultra-nationalist Vladimir Zhirinovsky's Liberal Democratic Party of Russia (LDPR) had 13.2%, reflecting its usual strong showing in the far east. That was likely to drop later as results from western areas were declared.
Motherland (Rodina), a new party combining left-wing economics with nationalism, made a surprise showing well over the 5% barrier required to win parliamentary seats.
Both LDPR and Motherland are expected to back the Kremlin, possibly giving it the two-thirds majority needed to change the constitution if it wanted to allow Putin a third term as president.
Sunday's results suggest Putin, a 51-year-old former KGB officer, is certain to win a second four-year term of office at presidential polls in March.
Police stand guard
Anatoly Chubais, whose liberal Union of Right-Wing Forces party may not pass the 5% barrier, said the results showed a dangerous shift towards fascism.
"It looks like the threat that we were the first to identify a week ago is becoming a reality," he said on state-controlled Rossiya television. "It is called national socialism."
The figures only apply to the half of the Duma's 450 seats awarded on the strength of national party lists. The remaining 225 seats are elected in individual constituencies and will be announced later in the week.
(Monday 0000 GMT)
1. United Russia 36.4
2. Liberal Democratic Party 13.2
3. Communist Party 12.9
4. Motherland (Rodina) 8.1
5. Yabloko 4.2
6. Agrarian Party 4.1
7. Union Of Right Forces 3.7
(% of votes counted: 34.94)
Armed police stood by all polling stations and thousands more were on guard in southern regions after 42 people died in a suspected suicide bombing of a train near Chechnya on Friday.
Putin called the attack an attempt to disrupt voting.
In high spirits as he cast his vote, he made clear his support for United Russia, created before the last election in 1999 to help his rise as Boris Yeltsin's chosen successor.
"My preference is well known," Putin told reporters.
In one of the few moments of passion in a drab election campaign, a protester shouting "Your elections are a farce" hit Prime Minister Mikhail Kasyanov with an egg as he was voting.