After repeated warnings for the crowd to put on their nose-and-mouth coverings went unheeded, police said they would take action to clear the protest and "detain violators".
As water was sprayed on the crowd, protesters chanted "shame, shame", refusing to leave the site.
Around 5,000 radical activists massed at the Brandenburg Gate, after the German government banned rallies outside parliament over police warnings the demonstration could turn violent.
The interior ministry said Tuesday it had been informed by security services that protesters intended to block access to the Reichstag and Bundesrat buildings, justifying the ban.
The Bundestag security force warned MPs that "demonstrators from politically radical and even violent groups" were expected to take part in Wednesday's protests with "attacks" possible.
Protest organisers accused the government of trying to establish a "dictatorship" with shutdown measures that were tightened this month to slow infection rates.
Demonstrators carried posters showing German political leaders including Chancellor Angela Merkel in prison garb and emblazoned with the word "guilty".
In online chatrooms, militant activists compared the government measures to the Enabling Act of 1933 which gave Nazi leader Adolf Hitler's government dictatorial powers.
The provocative comments drew outrage, with Foreign Minister Heiko Maas tweeting: "Those who make such disgraceful comparisons mock the victims of National Socialism and show they have learned nothing from history."
Selbstverständlich hat jede/r das Recht, die Maßnahmen zu kritisieren. Unsere Demokratie lebt vom Austausch verschiedener Meinungen. Wer allerdings den Holocaust verharmlost oder relativiert, hat aus unserer Geschichte nichts gelernt. #b1811 (3/4)
— Heiko Maas ?? (@HeikoMaas) November 18, 2020
MPs were set to grant state governments formal powers to limit social contact to help halt the spread of the virus, putting the shutdown measures on a firmer legal footing.
Several hundred aggressive demonstrators had already tried in late August to storm the Reichstag building where the Bundestag lower house meets during a rally against coronavirus rules, in a protest Merkel condemned as "shameful".
READ ALSO: Germany slams 'unacceptable' attempt to storm Reichstag building
The Bundestag security force warned MPs that "demonstrators from politically radical and even violent groups" were expected to take part in Wednesday's protests with "attacks" possible.
Achim Ecker, a demonstrator in his 50s who travelled to Berlin from neighbouring Brandenburg state, said the government was exaggerating the dangers posed by the pandemic.
"We don't need emergency measures," he said. "I believe in our own immune systems."
Earlier this month, more than 20,000 people joined a violent demonstration in the eastern city of Leipzig against curbs to control coronavirus infection.
Most participants refused a police order to disperse after ignoring requests to wear face coverings and keep a safe distance between participants.
Demonstrators attacked police and reporters, leading to 31 arrests. Political officials said that neo-Nazi supporters and extremist conspiracy theorists had helped incite the riots.
READ ALSO: German ministers condemn violence at Leipzig anti-mask protest
Germany has fared better than most of its European neighbours during the
pandemic, with polls showing broad acceptance of the government's measures to control the virus's spread.
But in response to a spike in infections this autumn, the country this
month shut down restaurants, leisure facilities and cultural sites to cut down on social contacts.
Merkel and leaders of the country's 16 states are to confer next Wednesday (November 25th) about a potential tightening of measures in the run up to the Christmas holiday period.
On Wednesday, the Robert Koch Institute for disease control reported 17,561 new cases over the last 24 hours, bringing total infections to date to 833,307.
At least 13,119 people have died from the virus so far.
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