During the demonstration, which police consider to have taken place calmly, an Israeli flag was set on fire.
The incident comes the day after reports of anti-Semitic chanting during a demonstration in Malmö.
The demonstration in Stockholm took place in reaction to US president Donald Trump's decision to move the American embassy from Tel Aviv to Jerusalem and recognise the latter city as the Israeli capital.
“There was an incident in which people joined the procession and took out a flag and began stamping on it. The organisers resolved it themselves,” Sven-Erik Olsson of Stockholm Police told TT.
TT’s photographer at the scene reported that people behind the demonstration noticed a man well behind the main group waving an Israeli flag. The people at the back of the group then rushed towards the man, before taking the flag and stamping on it.
It was later set alight by another group.
Photo: Jonas Ekströmer/TT
A demonstration in Malmö on Friday also caused uproar after the crowd was heard shouting anti-Semitic slogans.
That incident caused police to consider precautionary measures during Saturday’s protest in Stockholm.
“We deployed the manpower we felt was necessary. We make that type of assessment for all events of this kind,” Olsson said.
The demonstration, arranged by the Jerusalem Committee organisation, began at Humlegården in the Swedish capital early Saturday afternoon and ended in the Diplomatstaden area, where several foreign embassies are located.