The counter-demonstrators totalled 1,200, police spokesperson Judith Schnuphase told German newspaper Bild.
Meanwhile, around 120 people took part in the neo-Nazi march itself, which was roughly in line with expectations, the spokesperson said.
Because both sides had posted online to mobilise their members across Germany, the city and the police were prepared for considerably more participants on both sides.
The paper reported that there was a large police presence in Weimar, including officers from other states, such as Bavaria and Lower Saxony, as well as the federal police force, which had announced checks on train travellers at the station. A water cannon was in place near the station from Saturday morning.
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Some of the more radical counter-demonstrators tried to access the area where the far-right march was taking place multiple times, according to the police.
Around 25 officials from Lower Saxony were involved in scuffles in the process with police using pepper spray and batons to prevent this.
The pepper spray used also hit police officers, according to observations by a dpa reporter on the scene, Bild reported.
Some of the counter-demonstrators were expelled from the area, according to the police, and some violated the ban on face coverings.
A spokesperson for Mobit, a Thuringia-based initiative against far-right activity, said they were pleased so many people from different cities and regions in Germany were against the neo-Nazi march.
The attempt by the right-wing extremists to mobilise a larger number of “Querdenker” had apparently not been successful, they said.