Preliminary results showed the pro-Kremlin United Russia party, whose candidate list was headed by Putin, had received 64.1% of the vote allowing the president to retain power after leaving office in the spring.
"I want to thank Russian citizens, all voters, for a high turnout," the president said. "Special thanks to those who voted for United Russia, whose election list I headed, this is an indication of trust."
Putin said the polls showed that Russians would not permit the destruction of their country.
Russians would "never allow their country to follow the destructive path taken by some post-Soviet countries," he said in an apparent reference to street protests in Ukraine, Georgia and Kyrgyzstan, which brought pro-Western leaders to power.
In a televised speech on Thursday, Putin attacked opposition groups in Russia for receiving foreign funds and attempting to "bring back the time of humiliation, dependence and disintegration" Russia lived through in the 1990s.
Speaking on television, Putin said the State Duma, the lower house of parliament, to be formed after Sunday's election would be more legitimate than the previous one as it now enjoys greater voter support.
"The previous Duma was backed by 70% of the electorate, the new makeup has 90% of voter support, as just 10% of votes went for parties which failed to make it into parliament," he said.
Four parties overcame the 7% threshold to take seats in the State Duma, the fifth in the country's post-Soviet history. The Communists received 11.6%, the ultranationalist Liberal Democratic Party 8.2% and the loyalist A Just Russia 7.8% of the vote, according to results after 98% of the vote had been counted.
A joint statement by the Organization for Security and Co-operation in Europe (OSCE) and the Council of Europe said the poll "failed to meet many OSCE and Council of Europe commitments and standards for democratic elections."
Goran Lennmarker, president of the OSCE's Parliamentary Assembly, said Russia's new election law, which raised the threshold for entry to the State Duma from 5 to 7%, and also canceled "the against all" option and minimum voter turnout requirements, had created unequal conditions for smaller political parties.
He also said opposition parties had been pressurized. Shortly before the polls, two anti-Putin meetings in Moscow and St. Petersburg were dispelled by riot police and several opposition figures arrested, including former world chess champion Garry Kasparov, who was subsequently jailed for five days.
Lennmarker also said Putin's decision in October to head the United Russia list was the Kremlin's virtual merger with the party was unacceptable and violated international norms.