The disorder erupted as around 250 demonstrators from east Belfast returned from the city centre past a volatile community interface at the republican Short Strand.
Police said a number of missiles were thrown at the protesters from the Short Strand area, where around 70 youths had gathered.
The trouble soon spiralled from there as police moved up the adjacent Newtownards Road to separate rival factions.
Officers were attacked with petrol bombs, paint bombs, fireworks and heavy masonry while rioters damaged vehicles with hatchets and sledge hammers.
Protesters constructed a barricade in the middle of the road and set it on fire.
Police also received reports of an attempted car hi-jacking in the nearby Templemore Avenue area and attempted lorry hi-jacking in the Albertbridge Road area.
Police deployed water cannon and five baton rounds were fired. Calm was restored around 10pm.
The earlier demonstration at Belfast City Hall came as the council met for the first time since its controversial decision to limit the flying of the flag on the roof.
Loyalist protests have been continuing across Northern Ireland since early December in response to the vote by Belfast councillors to only fly the flag above City Hall on designated days instead of all year round.
The first of these days is this Wednesday, when the flag will be raised to mark the birthday of the Duchess of Cambridge.
More than 60 police officers have been injured in flag-related unrest in the last five weeks, with around 100 people arrested.
Last night, two males and two females were arrested in east Belfast for riot and public order offences.
Earlier yesterday Northern Ireland Chief Constable Matt Baggott claimed senior members of the paramilitary Ulster Volunteer Force (UVF) had been orchestrating the street violence in east Belfast.
Mr Baggott said there was no evidence that the organisation's leadership endorsed their actions.
Police also reported some disorder last night elsewhere in east Belfast, in the Dundonald area.
Last month, Sinn Fein, the Social Democratic and Labour Party (SDLP) and the cross-community Alliance Party all voted to limit the number of days the flag flies at City Hall, with all unionist members of the council opposing the move.
Since then, elected representatives from all sides and some representing areas beyond Belfast have received death threats. The latest was against SDLP Assembly member for Mid Ulster Patsy McGlone.
A parcel containing a sympathy card referring to Mr McGlone and a bullet was intercepted at a postal sorting office.
The flag issue was not on the formal agenda of last night's Belfast City Council meeting, but councillors did spend an hour debating the matter.
At the outset, DUP lord mayor Gavin Robinson urged members to show moderation in the discussion.
While some angry words were exchanged between councillors on opposing nationalist and unionist benches, the debate was generally even-tempered and well ordered.
Sinn Fein's Jim McVeigh accused unionist politicians of failed leadership and said they had allowed themselves to be "led by the nose" by a small band of extremists.
He said councillors would not be bowed by threats from loyalists.
"We won't be intimidated by those threats," he said.
"Their protests are pointless and they will have absolutely no impact on decisions that we take."
He said his party would respect British tradition but told unionists that respect was "not one way".
But his claims were met with a vociferous response from unionists.
Democratic Unionist councillor for east Belfast Robin Newton accused Mr McVeigh and Sinn Fein of "bulldozing" the flag vote through council.
"It was purely a political decision, a pure political decision," he said, rejecting the claims that unionists had not shown leadership.
But Mr Newton also called on loyalists engaged in the protests to seek a political route to voice their grievances instead.
"All sections of the unionist community should involve themselves in politics in Northern Ireland," he said.
Meanwhile, the organisers of a planned loyalist demonstration at Leinster House at the weekend have yet to make contact with gardai about the event.
The protest is intended to highlight the controversy over the decision to limit the number of days the union flag is flown over city hall.
Gardai are making contingency plans for this Saturday's protest in Dublin, despite the lack of contact from organiser Willie Frazer.
The demonstrators will be accompanied by uniformed gardai on Saturday as they line up outside Leinster House and their buses, meant to be confined to three, will be monitored as they travel into the city centre.
A number of public order units will also be on stand-by to prevent clashes between the loyalists and local objectors, who previously plundered building sites for weapons to use against loyalist marchers.
Gardai also hope to build up intelligence throughout the week on the likely reaction to the demonstrators.
Although the organisers said their group would be very limited in number, there are fears that if the current violence in Belfast escalates further, loyalist paramilitary groups could attempt to infiltrate the protest and exploit it for their own ends.
Tanaiste Eamon Gilmore said loyalists are welcome to take their protests against the removal of the union flag to Leinster House -- provided they do so peacefully.
An Oireachtas spokesman confirmed that the flag will not be flying on the day of the protest.
The Tricolour only flies over Leinster House when the Dail or Seanad is in official session.