Opposition leaders Alexei Navalny, Boris Nemtsov and Sergei Udaltsov were among those detained during violence that showed the depth of divisions and tensions in Russia as the former KGB spy starts his six-year third term on Monday.
"Putin has shown his true face, how he 'loves' his people - with police force," said Dmitry Gorbunov, 35, a computer analyst and one of many middle-class protesters who have joined protests against Putin in the past five months.
The violence came at the end of a day of protests in several cities against Putin, who will be sworn in at a lavish ceremony inside the Kremlin at which the head of the Russian Orthodox Church, Patriarch Kirill, will bless him.
Many of the protesters are angry that Putin is extending his 12-year domination of Russia, despite being undermined by protests, and fear he will stifle political and economic reform in his third presidential term.
They are also frustrated that the same faces will continue ruling the world's largest country and energy producer, ignoring the biggest protests since Putin rose to power in 2000.
Four years after Putin ushered his ally Dmitry Medvedev into the Kremlin and became premier in 2008 because of constitutional term limits, the two have agreed to swap jobs, with Medvedev set to take Putin's position as prime minister.
At least 20,000 people protested in Moscow under banners and flags, chanting "Russia without Putin" and "Putin - thief". Police said Udaltsov, Nemtsov and Navalny had been detained for "incitement to mass disorder".
Udaltsov, a leftist leader, was taken away as he tried to address the crowd from a stage and Navalny, an anti-corruption blogger, was dragged off after trying to organise a sit-in protest calling for Putin's inauguration to be scrapped.
In other protests, demonstrators carried a black coffin bearing the word "democracy" through the Pacific port city of Vladivostok. Several people were detained there and at protests in the Urals city of Kurgan and Kemerovo in western Siberia.
The Moscow protest was marred by the death of a photographer who Itar-Tass news said fell from a balcony as he tried to take pictures of the rally.
Health authorities said 20 police and 17 protesters sought medical help, including three police and 11 protesters who were hospitalised, Interfax reported. Most were later released.
The clashes were the worst since police moved in to disperse hundreds of protesters at or after rallies the day after Putin's March 4 election victory, which the opposition said was achieved with the aid of electoral fraud.
But the sting has gone out of protests since Putin, 59, won the election with almost 64 percent of the vote.
The former KGB spy simply ignored the protests. He looked relaxed as he attended a religious ceremony led by Russian Orthodox Patriarch Kirill that marked the transfer of a revered icon from a museum into the hands of the Church.
The demonstrations have deprived Putin of his aura of invincibility, and opposition candidates have been trying to get a foothold on power in municipal elections, but the size of the protests on Sunday was unlikely to trouble the president-elect.
Even so, protesters said Sunday's rallies were another signal to Putin that Russia had changed as he returns to the Kremlin after four years absence, even if change was coming slowly two decades after the collapse of the Soviet Union.