The Young Conway Volunteers band had been banned from parading past St Patrick's Church on Donegall Street in the city after being filmed playing an allegedly sectarian song at the spot during July 12 demonstrations.
Violence broke out in the area as the Shankill Road band marched past the church. A number of bands played music between Clifton Street and Unity Street area, which police also said was a breach of a ruling by the Parades Commission adjudication body.
It is understood police were attacked when they attempted to keep nationalists opposed to the parade and loyalists apart.
Bottles were thrown from both sides during the trouble. A female officer required hospital treatment after sustaining a head injury.
The 13-year-old boy was arrested in the Donegall Street area on suspicion of riotous behaviour. He was released pending a report to the Public Prosecution Service.
An 18-year-old man was arrested in the Clifton Street area on suspicion of disorderly behaviour and assault on police.
He has been charged with both offences and is due to appear at Belfast Magistrates Court on September 20.
A 38-year-old man arrested in the North Queen Street area on suspicion of disorderly behaviour and provocative conduct has been charged with both offences. He is due to appear at Belfast Magistrates' Court on Monday morning.