One male officer suffered facial injuries and a female officer sustained head injuries as individuals threw objects toward police and set fires at the scene in Forest Gate, east London, Scotland Yard said.
Four people were arrested for offences including disorder, arson and criminal damage in connection with the incident that began on Sunday evening.
Earlier crowds had joined a march demanding justice for Edir Frederico Da Costa, 25, who died on June 21.
He had been stopped in a car by Metropolitan Police officers in Newham, east London, six days earlier.
Campaigners claim Mr Da Costa’s neck was broken and he was “brutally beaten” after the car, containing three people, was stopped in Woodcocks, Beckton.
But the Independent Police Complaints Commission (IPCC), which is investigating, said a preliminary post-mortem on Thursday indicated there were no spinal injuries caused by police.
Protesters, some carrying Black Lives Matter posters and others with homemade placards which read “Justice for Edson + How Many More???”, marched from Forest Gate to Stratford on Sunday.
Borough Commander Superintendent Ian Larnder tried to calm tensions as he answered questions from organisers, telling the crowd: “I am here because l care deeply about what is going on.”
But a flurry of angry comments such as “you are protecting them” was hurled at Mr Larnder as members of the crowd pressed him about alleged police brutality.
“Police officers are all accountable to the law, they are being investigated,” he said.
When one of the campaigners asked if the officers involved in the incident were still working, he said: “I am pretty sure they have not been suspended but removed from operational duties.”
Protesters faced off against a line of uniformed officers at Stratford bus station, forcing some buses to be diverted, before marching back to Forest Gate police station shouting “we want justice” and “justice for Edson” to the beat of a drum.
The crowd arrived at the station at around 8.15pm where they were greeted by a cordon of uniformed officers at the entrance.
The atmosphere calmed as a minute’s silence was held at 8.40pm with the crowd holding clenched fists in the air.
But tempers flared again as the skies darkened and riot police wearing helmets and carrying shields pressed forward in a line from the police station at around 9.35pm.
Bricks were ripped from a wall and thrown at officers while firefighters, protected by police, hosed out a fire which had been set in a bin in Richmond Road.
Bins were also set alight near a McDonald’s in Romford Road, and a cordon of police, some with dogs, pressed demonstrators further down the street.
Family campaigners insisted the event had been set up as a peaceful march and they did not condone the violence.
Scotland Yard said Mr Larnder had “engaged with organisers in a bid to calm the crowd” before the protest returned to the police station.
A force spokesman said: “A number of objects were thrown towards officers. A small number of fires - involving the contents of litter bins - were also set in the street. These were quickly dealt with by the London Fire Brigade.
“At 10.50pm the size of the protest had significantly reduced but the protesters remained in the area.
“Shortly after 11.10pm, the main crowd dispersed into a number of smaller groups and again officers had items thrown at them.
“Six officers were injured, four of whom were taken to hospital for medical treatment. These include a male police sergeant who suffered facial injuries and a female police constable who suffered head injuries.”
There were no reports of injuries among members of the public or of “significant damage” to property, and the “vast majority” of protesters had dispersed by 3am on Monday.
The force said: “Four people have been arrested. One person was arrested on suspicion of disorder offences; three others were arrested on suspicion of arson and criminal damage.
“They have all been taken to east London police stations where they remain in custody.”