About 38,000 protesters gathered for events across the city and police reported pockets of unrest, as infections rise in Europe and public frustration at measures to contain the virus grows. Similar events took place in Paris, London and elsewhere on Saturday.
"Unfortunately, we have no other option," Berlin police said on Twitter, adding that those taking part had failed to comply with the safety conditions of the march.
At a demonstration close to Brandenburg Gate, several thousand were still gathered by early evening, some throwing rocks and bottles. Police arrested around 200 protesters, Berlin's interior minister Andreas Geisel said, describing the group as "extremist". Seven police were injured.
Nearby, a separate protest with about 30,000 was expected to carry on until 9pm (local time) because demonstrators were respecting the social distancing rules, Geisel said.
Police said 3000 officers had been deployed to control the crowds. Police had been preparing for possible violence as activists urged social media followers across Europe to arm themselves and gather in Berlin.
Berlin initially banned the protests but a German regional court overnight gave the final go-ahead by overruling the earlier decision.
Until now Germany has managed the Covid-19 crisis better than many of its European counterparts, with rigorous testing helping to hold down infections and deaths. There have been more than 9000 deaths so far.
But new daily infections have accelerated in recent weeks, as in much of the world.
On Friday, Chancellor Angela Merkel urged citizens to keep up their guard against the virus.
"This is a serious matter, as serious as it's ever been, and you need to carry on taking it seriously," she said.
Protesters had gathered before the Brandenburg Gate ahead of the march with signs reading "Stop the corona lies" and "Merkel must go".
Elsewhere in Europe, about 200 anti-mask activists held a rally in Paris to protest against sanitary measures with slogans such as "No to the health dictatorship" and "Let our children breathe".
In London, several hundred demonstrators gathered in Trafalgar Square calling coronavirus a hoax and demanding an end to restrictions.
Many carried banners saying "Fake News," or "Masks are Muzzles" and rejecting any mandatory vaccination programmes.
The virus has killed more than 40,000 people in Britain.
There were peaceful protests in Vienna and Zurich.
