The city centre protests come after disorder on 6 September, when police attended Eastney Marina as hundreds of demonstrators blocked roads in an attempt to stop coaches carrying 120 migrants, who had crossed the Channel in a dinghy, from leaving the city.
Up to 500 anti-migrant protesters held Union and St George flags while some wearing Portsmouth Patriot branded clothing gathered outside All Saints Church on Commercial Road shortly before midday on Saturday.
The crowd chanted “stop the boats” as they marched to Guidhall Square.
About 300 people joined the counter-protest.
Both sets of demonstrators were kept apart by police when they arrived at the square.
Speaking before the march, Simon Magorian, of Stand up to Racism Portsmouth, described the demonstrations in Eastney as a “horrible spectacle”.
He said: “Portsmouth is actually a good functioning multi-cultural city.
“We are now organising to have the broadest possible opposition to what we see as a fascist street movement and we’re not going to allow them to get a grip on Portsmouth or any other town – this is quite terrifying.”
Among the anti-migration protesters, Pete Davies, from Portsmouth, said he had also taken part in the demonstrations at Eastney.
“They should be having them turned back to France again. It’s a safe country, there’s no war in France.
“They want to stop the benefits, stop the free housing… they don’t give nothing back to the people of the country.”
Officers earlier said the powers were aimed at preventing violence, intimidation and disorder following protests in the city over the past week.
A separate order also allowed officers to require people to remove masks and other items used to conceal their identity.
Speaking on Friday, Assistant Chief Constable Paul Bartolomeo said: “It is important to stress that this power will apply to any groups that attend the protest and will be enforced equally and impartially.
“Let me be clear, these powers are not being implemented to prevent protest but they are being used to help prevent crime and disorder, while making communities feel safer.”
Hampshire Police said several of its vehicles, alongside those of the coastguard and Border Force, were damaged during the disruption, which lasted until the early hours of Monday.
It added that a small number of officers were treated at the scene for injuries but no-one in attendance was seriously injured.
RNLI volunteers involved in the operation to bring the migrants to shore were also targeted on social media.
The disorder in Portsmouth followed a separate anti-migrant protest at the Port of Dover the day before.