Counter-demonstrators also turned up in their thousands in Konstanz, southern Germany, to show support for the government's measures to contain the virus.
They were also protesting against the right-wing supporters in the other group, police said.
Between 10,500 and 11,000 people took part in the different demonstrations on Saturday, and they continued into Sunday with sunny weather likely to draw more participants, police said.
Organisers of the protest against restrictions had hoped more than 200,000 people would attend so they could make a human chain around Lake Constance on the border with Austria.
The counter-protesters formed a "peace chain" around part of the lake.
Local authorities have imposed measures such as social distancing to try to stem the spread of COVID-19.
They have also banned the use of Germany's imperial Reichsflagge, a symbol used by neo-Nazis and other far-right groups instead of the forbidden swastika flag.
A mix of civil rights activists, anti-vaxxers, neo-Nazis and members of far-right groups, including the opposition party Alternative for Germany (AfD), were in attendance.
These are not Germany's first restriction protests, with mass marches against coronavirus curbs taking place in Berlin in late August.
Protesters then stormed the steps of the Reichstag parliament building, some holding the Reichsflagge.
Images spread around the world and were condemned by Germany's leading politicians.
The country had managed the pandemic relatively well, with infections and deaths low compared with other European countries during the spring.
However, case numbers are rising again and authorities are considering further restrictions which would slow down Germany's economy after suffering its worst recession on record in the first half of 2020.