Trouble flared after a city centre demonstration against the council's decision to limit the number of days the Union flag is flown from City Hall.
Water cannons were deployed and a non-lethal baton round fired by riot police as they separated opposing factions amid a hail of bricks and fireworks at the Albertbridge Road near the nationalist Short Strand.
Earlier, nearly 1,000 people gathered at Belfast City Hall to protest.
Senior politicians from Belfast, Dublin and London are to meet next week to discuss the protests after more than 40 days of road blocks and sporadic violence by loyalists have failed to produce a solution.
Stormont First Minister Peter Robinson and his deputy Martin McGuinness will join Northern Ireland Secretary Theresa Villiers and Ireland's Tanaiste (deputy leader) Eamonn Gilmore.
Mr Gilmore said: "This violence is being orchestrated and those behind it are known criminals, intent on creating chaos.
"This has nothing to do with real issues around flags and identity in a shared society, which are the subject of intensive political discussions at present."
The demonstrations against Belfast City Council's decision to hoist the union flag from the City Hall only on designated days like royal birthdays have brought many parts of Northern Ireland to a standstill.
More than 70 officers have been injured and over 100 arrests made during weeks of sporadic trouble, the Police Service of Northern Ireland (PSNI) said.
Businesses in Belfast's city centre have struggled to cope, with many reporting lost trade, and the Confederation of British Industry (CBI) warned some investors may think again.
A doctor was prevented from attending a terminally ill cancer patient because of loyalist road blocks in south Belfast, it was revealed.
The GP was travelling to a home call with the sick man when he was stopped twice by crowds of demonstrators who blocked the road. Police asked them to move but they refused, nationalist SDLP MLA Conall McDevitt said.
He said: "These are depraved acts which immediately dismiss any claim on a protest being peaceful."
The doctor had to wait until the blockade was lifted.
A unionist forum chaired by DUP leader Mr Robinson and UUP leader Mike Nesbitt met last week to discuss ways of empowering loyalist working class communities.
A second peace rally is to be held outside Belfast City Hall tomorrow.