Carrie Lam, the city's Beijing-backed leader, told a press conference that the the ban on face masks, which are worn by many protesters to hide their identities, would come into effect at midnight local time.
"We've seen that almost all protesters who carried out vandalism and violence covered their face," Lam told reporters.
"We believe the prohibition on face covering regulation will be an effective deterrent to radical behavior and it will also help the police in enforcing the law,” she added.
If convicted, demonstrators could face a maximum fine of some 25,000 Hong Kong dollars ($3,187) and a year imprisonment, the Hong Kong information services department said in a statement.
If they refuse to comply with police to remove the face covering, a demonstrator could face a fine of up to 10,000 Hong Kong dollars ($1,275) and imprisonment for six months, the statement said.
Reasonable excuses for a person to cover their face include pre-existing medical or health reasons, religious or professional reasons, it added.
Before the new rule was confirmed, protests against it began across the Asian financial hub, with hundreds of office workers wearing masks gathering to march. Protests were happening in 16 districts, with many blocking roads and shutting down metro stations.
As of 9 p.m. local time there were no recorded clashes between police and protesters but riot police were on standby in different districts.
Protesters in Hong Kong’s Central district pulled down a banner celebrating the 70th anniversary of the People’s Republic of China from a bridge and set it on fire to the sound of cheers from onlookers.
Some demonstrators, chanted “rebel Hong Kong people” and “masking is not guilty, unreasonable legislation.”
Secondary school students wearing school uniforms could be seen among the throngs of people.
Lam said she was concerned by the number of students involved in recent demonstrations. From June to August, students accounted for around 25 percent of those arrested, she said, but since the start of school in September the proportion has now risen to 38 percent.
She said she hoped the ban would discourage young people from taking to the streets.
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But young Hong Kongers who spoke to NBC News said they would continue to protest and cover their faces.
Aki Chi, a 29-year-old sound actor who was headed to a demonstration in the city's Central district, said he “absolutely” would not comply with the new ban.
“I have no intention to respect it,” he told NBC News.
IN #HONGKONG: Carrie Lam says the new face mask ban does not suggest a state of emergency, but is a move to gain control over ‘riots’. In August, she rejected the idea, fearing it would backfire and further damage the city’s reputation. @NBCNews@MSNBC (video source: me/Sept30) pic.twitter.com/LVWcaZEJgN
Jane Chiu, 23, said the ban allowed the police more power on the streets and proved the government was attempting to suppress the voices of its citizens.
“This is authoritarianism, welcome to just another Chinese city,” she said.
The H.R. worker added that she also would not stop wearing masks to protests.
“If we allow this to happen, we are just opening our doors to any other possible regulations in the future."
Many people in Hong Kong wear masks on a daily basis to protect themselves from colds and flu. Lam said she had taken this into account.
"The regulation will target those who use violence, we understand there may be other people who need to wear a mask or cover their face because of a legitimate need," she said.
However, it remained unclear how the government planned to enforce the ban or how straightforward it would be to evaluate "legitimate" use.
Lam stressed that the new regulation did not mean that Hong Kong was in a state of emergency but said it was experiencing a moment of "rather extensive and serious public danger."
"I hope the public will support and understand what we're doing," she said.
Many do not. Prominent activist Joshua Wong tweeted that Friday's announcement could lead to further powers, such as arbitrary arrest.
1/ It is no less harmful than the extradition bill as virtually the law gives CE mighty power to impose whatever she & Beijing like to — more arbitrary arrest and search, extending dention to 96 hours or more, banning internet access, de facto martial laws are highly expected.
The protesters are angry about what they see as creeping interference by Beijing in their city's affairs despite a promise of autonomy in the "one country, two systems" formula under which Hong Kong returned to China in 1997.
China dismisses accusations it is meddling and has accused foreign governments, including the United States and Britain, of stirring up anti-China sentiment.
Lam said Friday that so far some 1,100 people had been injured and of them around 300 were police officers in the violence.
What began as opposition to a proposed extradition law, which could have seen people sent for trial in mainland courts but has now been shelved, has grown into a call for five demands, including universal suffrage and an inquiry into alleged police brutality.
Protesters, some wearing gas masks and helmets, marched past some of the city's most expensive real estate including British bank HSBC's head office, on Friday, calling out for "five demands, not one less".
Riot police moved in to districts across Hong Kong overnight, firing tear gas at a chanting crowd in a residential area, while rail operator MTR Corp shut several stations as violence escalated.
Police said the officer involved in the shooting acted in self-defense because his life was under threat. The teenager, the first protester hit by live fire during months of unrest, remains in hospital in a stable condition.
Lam said Friday that escalating violence, use of lethal weapons and snatching of police pistols meant police have "no choice but to use guns to try to save their own lives."
Saphora Smith is a London-based reporter for NBC News Digital.
Patrick Smith is a London-based editor and reporter for NBC News Digital.