The electoral commission declared Putin the victor with 63.7% of the votes with nearly 100% of the ballots counted. But Putin's opponents refused to recognise the results and said they would press ahead with the biggest protests since he rose to power 12 years ago.
But the former KGB spy said he had won a "clean" victory and was on course to return to the Kremlin after four years as prime minister.
"I promised you we would win. We have won. Glory to Russia," Putin, dressed in an anorak and flanked by outgoing President Dmitry Medvedev, told tens of thousands of flag-waving supporters at a late-evening victory rally under the red walls of the Kremlin.
Denouncing attempts to "destroy Russia's statehood and usurp power", he said: "The Russian people have shown today that such scenarios will not succeed in our land ... They shall not pass!"
The crowd at one point chanted: "Putin! Putin! Putin!" Some danced to keep warm and drank vodka from plastic glasses, with empty bottles crunching underfoot.
It was a defiant and angry speech which left Putin, 59, on collision course with the mainly middle-class protestors in Moscow and other big cities who have staged huge rallies since a disputed parliamentary poll on 4 December.
'Declaration of war'
His nearest rival, Communist Party leader Gennady Zyuganov, had about 17% of votes, and nationalist Vladimir Zhirinovsky, former parliamentary speaker Sergei Mironov and billionaire Mikhail Prokhorov were all below 10%, although Prokhorov won plaudits for his campaign.
Zyuganov said his party would not recognise the result and called the election "illegitimate, dishonest and untransparent". Liberal leader Vladimir Ryzhkov also said it was not legitimate.
The protest organisers, who see Putin as an autocratic leader whose return to power will stymie hope of economic and political reforms, said their demonstrations would now grow.
"The social base of the protest is going to grow and Putin with his team did everything wrong to make this happen. He really helped us," said journalist Sergei Parkhomenko, one of the leaders of the opposition protest movement.
"He is forcing things to breaking point. He is declaring war on us. As a result the base of aversion to him is growing."
Thousands of opposition activists as well as an international observer mission monitored the polls.
Vote monitors from the opposition and bloggers posted allegations of election rigging across the country of 143 million. Golos, an independent monitoring group, said it had registered at least 3,500 reports of violations nationwide.
Despite the opposition, mainly among well-educated and relatively well-off young professionals, Putin's support remains strong in the provinces and his victory had not been in doubt.
He showed his gratitude in late-night video links with supporters around Russia, including workers at a tank factory in the Urals town of Nizhny Tagil who have denounced the protests.
"You put in their places those people who went one step too far and insulted the working man," Putin told them. "You showed who the Russian people are, the Russian working man, the worker and the engineer. You showed that you are a head higher than any layabout, any old windbag. This was for me the biggest present."
A spokesman later said Putin had wept real tears at the victory rally but said they were caused by the biting wind.
But the reaction to his rallying cry at the victory rally was more muted than expected. Hundreds of buses had brought the crowd to Moscow, signalling that it was a well-organised show of force rather than a spontaneous display of support.
The mood has shifted in the country and many people are uncertain whether he will be conciliatory and reformist, or stand in the way of political and economic change.
Putin, who will be inaugurated in May, is likely to revert to the fighting talk against the West that was the trademark of his first presidency and his election campaign.