Television and user-generated video footage showed Interior Ministry (OMON) riot police moving into the square to detain or brutally eject at least 200 of protesters who remained past the scheduled conclusion of the sanctioned rally.
Opposition leaders Sergei Udaltsov, Ilya Yashin, and Aleksei Navalny were reportedly among those detained. All three -- along with other detainees -- were scheduled to appear in court on March 6 to face charges connected with the protest.
Navalny and Udaltsov were reportedly charged with administrative offenses and faced fines of up to 2,000 rubles (some $70) each. Yashin was charged with violations over the holding of the rally and faced up to 15 days in jail.
Police detained some 250 people in Moscow.
Authorities also arrested some 300 in St. Petersburg, at another anti-Putin protest.
Dozens of journalists gathered at the Moscow site were briefly detained or roughly removed from the square. Drivers passing by the site honked their horns noisily to protest the heavy-handed tactics of the OMON forces.
A number of protesters were seen being dragged from the protest site with their arms pinned behind their heads, an OMON officer on either side.
The crackdown comes after as many as 20,000 Russians gathered in central Pushkin Square to call for fresh elections to replace the March 4 polls, which handed Putin a sweeping victory with almost 64 percent of the vote.
PHOTO GALLERY: Scenes From The Protests
Gathering amid a heavy police presence, protesters shouted "Shame!" and protested Putin's win, which puts him in position to dominate the country's political scene through 2024.
Sasha Primakova, a 32-year-old mother of two, was among those participating in the Pushkin Square protest before the breakup.
Primakova, a marketer, told RFE/RL she has been attending the anti-Kremlin protests since December, when heavily criticized parliamentary elections handed a win to Putin's ruling United Russia party and prompted a groundswell of public opposition.
She said the presidential election was like a slap in the face.
WATCH: Eduard Limonov, the head of the Other Russia opposition coalition, is arrested. (Video by RFE/RL's Russian Service)
"We do not consider the presidential elections that took place to be legitimate and we've come here in protest," she said. "There were a lot of falsifications and violations, but they used different methods that are harder to spot."
The late-night crackdown, which followed a season of peaceful opposition protests, may signal that authorities' tolerance for public dissent may be waning now that Putin's election is secure.
But Aleksandr, a 48-year-old production manager, said it was key for protesters to continue coming out onto the streets to make their voices heard.
"Everyone who wants to live in a normal Russia and everyone who wants changes for the better have to be with the people who are organizing these protests now," he said.
A triumphant Putin described his victory as clean and fair. But Western monitors on March 5 said the run-up to the elections was heavily biased in favor of Putin and virtually absent of true political competition.
Volunteer election monitors also claim the vote was riddled with numerous instances of voter fraud.
WATCH: Police break up an anti-Putin rally in St. Petersburg. (Video by RFE/RL's Russian Service)
Bakhlon, a 21-year-old law student at Moscow State University, was among the volunteer election observers and attended the Pushkin Square protest.
"Putin has already been humiliating Russia for exactly 12 years. If it continues like this, Russia is going to descend into chaos," he said. "That's why I want clean elections. The elections that just took place were not fair. I'm 100 percent sure of that."
Dozens of protesters at a separate demonstration outside the Central Election Commission were reported arrested, including Eduard Limonov, the head of the Other Russia opposition coalition.
At the same time, numerous pro-Putin demonstrations were held throughout Moscow.
Leaders of what they have dubbed the "non-system opposition" are planning fresh coordinated protests on March 10, RFE/RL's Russian Service reports.