Two officers had to go to hospital, while a further two security staff members and a press photographer were also injured on Monday night.
It came after a controversial vote was passed to fly the Union flag only on designated days at City Hall.
Up to 1,500 loyalists gathered outside the building for what began as a peaceful protest, but when news of the outcome came through, crowds tried to smash their way into the grounds through the rear gates.
Sporadic violence then spread across east Belfast, with reports that St Matthew's Catholic Church on the Newtownards Road came under attack.
Police said reinforcements had to be called in to deal with hundreds of people throwing missiles, including fireworks, bricks and bottles.
There were reports of damage to homes in the Strand Walk area and a double decker bus was also attacked during an attempted hijacking on the Albertbridge Road. Officers prevented it from being badly damaged.
Three arrests were made in the wake of the violence.
Police questioned a 17-year-old suspected of rioting on the Albertbridge Road, and a 22-year-old suspected of assault and doing a provocative act in Donegal Square.
They have been released on conditional bail, pending further inquiries.
Police also detained an 18-year-old on suspicion of riotous behaviour and possessing a petrol bomb in Clandeboye Street - he has been reported to the PPS.
First Minister Peter Robinson described the violence as "unacceptable".
The DUP leader said: "The scenes of violence in and around Belfast City Hall and the wider vicinity are totally unacceptable and must be unreservedly condemned."
There is no excuse or justification for attacks on police officers, council staff, and property.
First Minister Peter Robinson
"Such behaviour is not representative of those who campaigned to maintain the Union Flag flying over Belfast City Hall. My thoughts are with those police officers and security personnel who have been injured as well as those whose property has been damaged and I would appeal to the community to remain calm and not to get drawn into confrontation."
Sinn Féin Policing Board member Gerry Kelly said the PSNI had serious questions to answer about their security operation.
He said: "I have to say, and I don't use these words unless I really mean them, it was a disgraceful police operation - or lack of a police operation.
"If that had been 1,000 or more republicans out there ... they would not have left it that they were able to come into the back of City Hall.
"They indiscriminately attacked cars. We are very, very lucky that they didn't get into the building or we could have been dealing with a lot more injuries."
Chief Superintendent Alan McCrum defended the PSNI's response.
He explained: "A diverse crowd, of up to 1,500 at the peak of the protest, consisting of men, women, young people, mothers with children in buggies and wheelchair users gathered at the back of City Hall.
"Police had no definitive intelligence to suggest that there would be any violence and given the diversity of the people protesting, the operation had to be managed very carefully.
"Neighbourhood officers who had been positioned outside the gates of City Hall were attacked and these officers were then replaced with riot police who were located a short distance away on the other side of the road.
"Officers had also been positioned inside the quadrant area at the back of City Hall to prevent those individuals who breached the gates from entering the building.
There is no excuse for vandalism and thuggery in a democratic society.
Chief Superintendent Alan McCrum
"This disorder was completely disgraceful. People have the right to lawful protest, but democracy has a right to be protected."
SDLP councillors said they met Mr Crum on Tuesday to discuss their concerns.
Tim Attwood said: "My colleagues and I were deeply concerned for the welfare of council staff, police officers, journalists and members of the public who were in the vicinity of City Hall. We were deeply disappointed that there was not a police presence inside the building itself to assist council security workers and other staff."
The chairman of the Policing Board condemned the disorder and said members will discuss the PSNI's preparations when they meet on Thursday.
Brian Rea said: "This disorder was completely inexcusable and the violence around and directed at the civic building of our capital city absolutely disgraceful. Police officers, council staff and others have been left injured and I send them all best wishes for a speedy recovery.
"Questions have been raised around the preparedness of the PSNI and Board Members will have an opportunity to discuss the policing operation with the Chief Constable on 6 December."
The trouble flared up shortly after councillors decided by 29 votes to 21 in favour of ending the policy of flying the Union flag all year long at City Hall.
When the flag was taken down early on Tuesday morning it marked the first time it first time it stopped flying over the historic building since it opened over a century ago.
Nationalists wanted to remove it altogether, however an Alliance Party amendment means it will now fly on 17 designated days, in line with Stormont.
It comes after the council's strategic policy and resources committee voted 11-9 in favour of removing the flag completely last month - a move supported by Sinn Féin and the SDLP.
Unionist politicians did not back the proposals.
Alliance leader and Justice Minister David Ford described the result as "a clear victory for the Alliance Party".
The violence which took place at the City Hall and round St Matthew's Church was the responsibility of two groups of people. The first is those who went to the City Hall spoiling for a fight, who attacked police officers and council staff.
Justice Minister David Ford
He condemned the violence, saying: "But there is a second group which bears responsibility. DUP and UUP politicians fomented this protest, with both leaflets and the use of social media.
"They called people on to the streets. They must have known, from experience as recent as this summer, that violence was almost inevitable. They cannot avoid their responsibility.
"Such violence should be condemned by all civic and community leaders."
Meanwhile the leader of the Progressive Unionist Party, Billy Hutchinson, questioned the motive behind calls to take down the flag.
He said: "Sinn Féin are quick to use the language of parity and equality, yet where is the equality here when citizens of the United Kingdom are denied the right to have their national standard raised over a seat of local government."
"This issue around the flying of a flag is part of a wider attempt by Sinn Fein, and nationalism in general, to undermine unionist culture and traditions.
"The summer of discontent created by republicans during the marching season is threatening to carry on through the winter. However, this says as much about the freeze they are feeling in their communities and their own lack of confidence in the face of a confident unionism."
UUP leader Mike Nesbitt said: "What we saw last night was wrong on two levels.
"The violence was wrong, but so were the circumstances that gave rise to the street protest, and that is the political failure to agree a Shared Future. For the Ulster Unionist Party that means agreeing a way of working and living together that affords mutual respect.
"It is not about everyone becoming the human form of beige and abandoning our history, our heritage and the values that for Unionists are embedded in the Union Flag."