The MND march, officially to protest the Czech military presence in Iraq, had been banned after a series of court judgements.
However the group still held the protest, arguing that authorities had offered no alternative routes and that they had a right to express their political views.
The march fell on the anniversary of Kristallnacht, or Crystal Night, in 1938, when Nazis across Germany and in parts of Austria ransacked Jewish homes, shops and synagogues and killed more than 100 Jews.
The march was condemned by several politicians, including Pavel Bem, the city's mayor, who was present at the counter-demonstration.
"We need to cultivate the national memory to avoid what happened in the past," he said.
Czech authorities had ordered tighter border controls after reports that neo-Nazis from neighbouring countries could attempt to enter the country and attend the march.