Two police vehicles, two privately-owned vehicles and a shop window were also damaged during the trouble.
A 16-year-old youth and a 25-year-old man have been arrested and are being questioned by police.
Earlier around 150 people gathered at the Town Hall in the Linenhall Street area to express their anger after the flying of the Union flag was restricted at Belfast City Hall.
TUV leader Jim Allister attended the protest.
Most of the crowd later dispersed and only a small number remained in the area when disturbance erupted.
Police said they liaised with local community representatives in their efforts to restore calm.
Local Area Commander Chief Inspector John Magill said it was "encouraging the protest itself was largely peaceful".
He said police will be actively pursuing those who were involved in the disorder and an inquiry team has been established.
Earlier on Thursday a number of people gathered in the Antrim Road area of Glengormley and outside the Alliance Party offices in east Belfast, causing traffic disruption to motorists.
Two men aged 27 and 21 have been charged with a number of public disorder offences in connection with the protest and are due to appear before Belfast Magistrates' Court on Friday.
First Minister Peter Robinson has called for an immediate end to violence over the issue of flags and the suspension of street protests, in order to prevent peaceful demonstrations being hijacked.