Protesters marched from the landmark Brandenburg Gate through central Berlin before holding a rally on a wide boulevard.
Police filed a complaint against the organiser for failing to ensure marchers wore masks and kept their distance.
Protesters who came from across the country held up homemade signs with slogans like "Corona, false alarm", "We are being forced to wear a muzzle", "Natural defense instead of vaccination" and "We are the second wave".
People voiced opposition to protective measures with whistles and chants like "freedom" or "resistance".
The protest, declared as "Day of Freedom", was supported by some neo-Nazi groups and conspiracy theorists, along with Germans who say they are fed up with the government's restrictions to curb the pandemic. A handful of counter-demonstrators also gathered, many under the banner "Grandmas against the right", and shouted "Nazis out" at those taking part.
But protesters on Saturday said those restrictions had trampled their rights. Police stated the event was over as organizers again failed to get protesters to wear masks or keep their distance.
Reporting from Berlin, Al Jazeera's Dominic Kane said the demonstrations are being felt most in "ministerial circles", with federal and state officials fearing the gathering may catalyse a rise in new infections that has already begun, with new daily case numbers the highest since May.
Restrictions in Germany include the wearing of face-coverings in shops and on public transport, social distancing rules and hygiene requirements apply throughout the country.
On Friday it recorded more than 900 new cases and seven deaths. Amid concerns that residents bring infections to homes from summer trips overseas, officials presented free tests for people entering the country.
Reacting to the protest march via Twitter, Saskia Esken, the co-chairwoman of the co-ruling Social Democratic party (SPD), lambasted the demonstrators calling them "Covid idiots for celebrating the second wave in Berlin" without observing the social distancing rules and wearing a face mask.
"They are not only jeopardizing our health, they are jeopardizing our success against the pandemic and for the revival of the economy, education and society".