Police were attacked with stones and bottles last night and petrol bombs were thrown at houses and a church in the neighbouring Catholic Short Strand district where people attending a special needs meeting fled in terror.
The bus driver was believed to have been hurt by flying glass when a brick was thrown through his window in the lower Newtownards Road area.
He was taken to hospital for treatment for cuts to his face, the Police Service of Northern Ireland (PSNI) said.
Police used water cannon to help restore order, and one officer was injured.
A 17-year-old boy was arrested, and two men aged 70 and 26 were detained in a separate incident connected to disorder which followed a flag protest in the Great Victoria Street area.
Bomb disposal experts also carried out a controlled explosion on a suspicious object in Bradley Way, Strabane.
Trouble in Belfast flared just hours after the Chief Constable Matt Baggott and politicians on all sides appealed for calm. Business leaders also warned of the disastrous impact on trade.
A number of roads were blocked for a time yesterday. Some motorists held up in long tailbacks complained that police failed to take tougher action to clear masked demonstrators waving flags.
Bus services in the east of the city were also suspended immediately after the hijackings and just before loyalists attacked houses and St Matthews Catholic Church in the Short Strand.
Nobody was hurt, but neighbours claimed frightened people attending a special needs meeting in an adjoining parochial hall had to run for cover.
A major conference of teachers planned for the city next November has been cancelled because of the continuing disorder - now in its seventh week - in protest at a decision to restrict the flying of the Union flag above City Hall.
Conall McDevitt, an SDLP member of the Northern Ireland Assembly and city councillor who voted for the flag to be lowered, said it was an unprovoked and unjustifiable attack on people's homes and a place of worship, and there could be no explanation for such depraved acts of violence.
He said: "This behaviour is as sickening now as it was when it first started - and more so, because the perpetrators know that they have no legitimacy and waning support.
"This is not a cause - this is simply the worst depths of human nature run amok."
Earlier yesterday senior police and politicians united in their demands for an end to the violent protests.
The First Minister Peter Robinson branded rioters the enemies of democracy and claimed they were being exploited by elements seeking to wreck the peace process.
"You do not respect a Union flag if you are using it as a weapon to charge against someone," he said.
"You are not showing respect for the Union flag if you need to wear a mask when carrying it.
"For many the issue of the flying of the Union flag at Belfast City Council is now a cynical cover for the real political agenda which is to destroy the political process."
Civil unrest has erupted in parts of Northern Ireland since Belfast City councillors voted on December 3 to restrict the number of days the Union flag would be flown over City Hall.
To date 101 police officers have been injured, one of whom is still in hospital.
There have been 112 arrests and 85 people, including a number of children, have been charged with public order offences.
The bill for policing the riots has already exceeded £7 million.
Mr Baggott has called for politicians to act quickly to resolve the crisis.
He revealed his commanders on the ground were revising their tactics, but said sweeping protesters off the streets was not a realistic option.
He said: "Even when the PSNI was 12,000 strong it would not have been possible to take such a rigid approach towards protests. Our approach has always been to be measured and responsible.