Stuttgart police would not estimate the size of the crowd, but said the gathering went off without incident and that demonstrators largely kept the required distance from one another.
Ballweg has said his "Querdenken" movement, a name which translates roughly as "lateral thinking," is calling for the restoration of fundamental rights such as freedom of assembly and freedom of religion.
The tech professional was initially banned from holding the demonstration by the city, but Germany's Constitutional Court overturned the ban.
In the capital Berlin, police said around 300 protesters gathered at Rosa-Luxemburg-Platz in the central Mitte district.
City police had only approved two protests of up to 20 participants each.
Registered outdoor gatherings are allowed in Berlin of up to 20 people. From Monday this rule will be relaxed to allow groups of up to 50 people.
German President Frank-Walter Steinmeier said he is watching the attempts of politicians to strike a balance between protecting the population and providing relief from the restrictions.
That the country was now experiencing fewer new daily infections was the result of "intelligent crisis management, coupled with the responsibility and discipline of the people in Germany", he said.
If the restrictions were now to be lifted too quickly, "we would have won a Pyrrhic victory", he warned.
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