Commissioner Cressida Dick was among hundreds who took part after a van hit worshippers near the Muslim Welfare House mosque and community centre.
Ramadan prayers took place on Monday after worshippers broke their fast, but leaders said it was quieter than usual.
Darren Osborne, 47, from Cardiff, has been held on suspicion of attempted murder and alleged terror offences.
The Metropolitan Police said he was being held on suspicion of the commission, preparation or instigation of terrorism including murder and attempted murder.
His family members have said they are ""shocked" and "devastated".
Mr Osborne's mother, sister and nephew said in a statement: "We are massively in shock, it's unbelievable. It still hasn't really sunk in."
They added that their "hearts go out to those who've been injured".
The attack took place shortly after midnight on Sunday night, close to Muslim Welfare House on Seven Sisters Road.
The driver of the van was detained by bystanders before police arrived.
Nine people were taken to three London hospitals after a van struck pedestrians. Two were treated for minor injuries at the scene.
Several of the injured are believed to be seriously hurt.
Those who were injured had been helping a man who had collapsed. He later died but it is not clear if that was because of the attack.
Faith leaders addressed a crowd at the vigil outside nearby Finsbury Park Mosque. People from across the community had gathered in solidarity and to lay flowers.
After a short silence, chairman of the mosque Mohammed Kozbar told those attending that the attack was "on our families, on our freedom, on our dignity".
He said the man who died was a father of six children.
The Bishop of Stepney, Rt Rev Adrian Newman, said "an attack on one faith is an attack on us all".
Ms Dick said the incident was "quite clearly an attack on Muslims", and the community would now see more police, including armed officers, in the area, "particularly around religious establishments".
Later, Muslim worshippers attended midnight prayers. At the scene, the BBC's Simon Clemison said: "People came to prayer just as they would have done.
"It was pretty full - although one of the leaders of the mosque said it was quieter, he felt, quieter for one of the busiest times of Ramadan."
He said there were some reservations amongst worshippers, about the media, and about decision-makers.
But there was also positivity as people came from other parts of the capital to pray with the community.
The government is working to tackle hate crime and "all forms of extremism" the home secretary has said.
Writing in the Guardian, Amber Rudd said: "We must unite the might of community spirit and the full force of the law to ensure every person in the UK is protected. Let there be no doubt we will be tough on terror wherever it strikes. And last night's attack was terrorism."
She said this latest "attack on Britain" united everyone in grief and anger, adding: "It is vital, now more than ever, that we stand together and do not allow people who seek to use hate to divide us to succeed."
Security Minister Ben Wallace said the suspect was not known to the security services, and was believed to have acted alone.
The BBC understands Mr Osborne grew up in Weston-super-Mare, Somerset, and has lived at more than one property in Cardiff. He is also believed to have lived in Swindon.
Police searches are being carried out in the Cardiff area.
It is the fourth terror attack in the UK in three months, after incidents in Westminster, Manchester and on London Bridge.
Prime Minister Theresa May said the attack was "every bit as sickening" as the others. She visited Finsbury Park Mosque on Monday and held talks with faith leaders.
Labour leader and Islington North MP Jeremy Corbyn also visited the area, telling the BBC that "an attack on a mosque, an attack on a synagogue, an attack on a church is actually an attack on all of us".