A PSNI spokesman said four officers were taken to hospital after police came under "heavy and sustained" attack during disturbances in the area on Saturday.
Two have been discharged, while two are still receiving treatment for their injuries.
Violent clashes first broke out between loyalist and nationalist crowds near the Short Strand area, where a number of homes were attacked and windows were smashed, after the city centre protest.
Rocks, bottles and fireworks were thrown at police when they moved in to separate the rival crowds amid reports of hand-to-hand fighting on Saturday afternoon.
Six baton rounds were fired and water cannon was also deployed.
Police also came under attack in the Castlereagh Street area, while a car was set on fire at the junction of Castlereagh Street and Templemore Avenue as sporadic trouble continued into the night.
Earlier politicians and community workers from both sides attempted to restore calm on the Albertbridge Road.
Loyalist community worker Jim Wilson said the police decision to block the Queen's Bridge as loyalists protestors were returning from the city centre resulted in disturbances.
It saddens me that once again in east Belfast we have trouble on the streets.
"I warned them (police) that this possibly could happen," he explained.
"I said to them if they do not let them through then they will take an ulterior route and the problem is they took an ulterior route and they came round this way and then police were not prepared for that."
Loyalist community worker Alfie McCrory also questioned the decisions taken by police on Saturday afternoon.
"Forty landrovers on this side and none on the inside," he said pointing to the Short Strand area.
But police claim flag protestors had been made aware that they should move out of the city centre via the Queen Elizabeth II Bridge and Middlepath Street, therefore bypassing part of the Short Strand.
Officers closed off the adjacent Queen's Bridge and were working with marshals when they say loyalist protestors, who were trying to cross the bridge, broke away and ran down Oxford Street, splitting at Lanyon Place.
"Some individuals ran along the Laganbank Road while others ran along East Bridge Street. At this stage many put on masks and covered their faces," a PSNI spokesman added.
Police say they then came under attack from bricks, stones and other missiles.
This was a difficult operation dealing with a large number of people determined to cause disorder and violence.
As the loyalist protestors approached the Short Strand, police said missiles were thrown by "rival factions" across the interface and a number of homes were damaged at the flashpoint.
PSNI Chief Constable Matt Baggott praised the work of his officers in a "difficult" situation.
"My colleagues brought the situation under control with exceptional courage and professionalism," he said.
"I know the vast majority of people will be grateful for their efforts. Police will continue to engage with all those committed to finding a solution to these issues."
Local Sinn Féin Councillor Niall Ó Donnghaile said tensions are running high among Short Strand residents after five weeks of loyalist protests in the area.
"What has been allowed to happen here is an absolute disgrace and now we as a community have to deal with the fall-out of illegal protests, anti-democratic protests and people who simply cannot tolerate the fact that the Short Strand as a community exists," he said.
Short Strand resident Barry Reynolds spoke to UTV after his home was damaged during the rioting.
He says bricks were put through his window as his 15-year-old son watched TV.
He is angry at police after the attack. "It's a disgrace... Why can't they sit here and protect us?" he said.
A number of homes along the Albertbridge Road are seriously, seriously damaged. That's the impact of an illegal parade.
Niall Ó Donnghaile
Earlier flag protestors gathered at Belfast City Hall to show their ongoing objection to the council's decision to limit the flying of the Union flag to 18 designated days.
They came from across Belfast and further afield to take part in the weekend demonstration, which has been held each Saturday since the vote was taken in December.
There was a low-key police operation surrounding the protest at city hall, which passed off without incident.
Public transport into and out of the city was disrupted and Translink said a number of bus services were also suspended on Saturday.
On Saturday evening, police confirmed they were also aware of a peaceful protest on the Antrim Road into Ballymena.
It comes after violence broke out in Newtownabbey where four police officers were injured on Friday night. Rioting also flared in Carrickfergus.
It followed six consecutive nights of violence in east Belfast earlier this month.
The Confederation of British Industry has revealed the flag dispute has cost businesses in Belfast up to £15m.
Local traders are expected to ask local politicians for a bailout at a meeting of business owners planned for next week.
A peace rally will be held in the city centre on Sunday afternoon.