"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."
The Independent Police Complaints Commission (IPCC) is investigating the treatment of Mr Da Costa, who died six days after he was stopped by police and detained on June 15.
One male officer suffered facial injuries and a female officer sustained head injuries as protesters hurled objects towards riot police and set fires in Forest Gate, east London, Scotland Yard said.
Scotland Yard added that four people had been arrested follow the clashes, which came amid claims a young father was beaten to death by officers.
Campaigners shouted "we want justice" as they stood toe-to-toe with riot cops to allege Edir Frederico Da Costa was "brutally beaten" after the 25-year-old was stopped by police.
Tensions spiralled in a clash at Stratford bus station yesterday afternoon before street fires were started and cars set alight after crowds marched to a police station just a mile away in Forest Gate.
Videos of small fires littering the roads in East London accompanied the hashtag "Justice for Edson", following on from the earlier protests.
One demonstrator earlier rode his motorcycle riot up to a line of officers and revved his bike, sending smoke billowing into their faces.
Bins were set on fire on the Romford Road as by midnight the group of angry protesters was said to have reached 200.
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.
Edir Frederico Da Costa, 25, died days after being arrested in London
On Friday it posted a statement on Twitter, which read: "Today we have contacted Mr Da Costa's family to share with them the findings from the pathologist and we are now able to correct some misinformation that is being widely shared on social media.
"The preliminary post mortem found that Mr Da Costa did not suffer a broken neck, or any other spinal injury during his interaction with the police."
However Scotland Yard believes Mr Da Costa swallowed a "large quantity" of drugs, which could have led to his death.
Borough Commander Superintendent Ian Larnder faced the angry crowd as he answered questions about the death on Sunday afternoon.
Campaigners claim his neck was broken and he suffered head and other injuries after he was stopped in a car, with three other people, by Met officers.
A flurry of angry comments such as "you are protecting them" and "you have told us what you can't do, now tell us what you can do" were hurled at Mr Larnder as members of the crowd pressed him about alleged police brutality.
More questions and disbelieving comments drowned him out as he told the crowd: "I am here because l care deeply about what is going on."
He also said: "Police officers are all accountable to the law, they are being investigated.
"I genuinely feel for you. I will ring the IPCC and ask them what are you doing."
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."
The crowd later began marching to Forest Gate police station shouting "we want justice" and "justice for Edson" to the beat of a drum.
It was reported bricks were pulled from a wall and thrown at police as the family of Mr Da Costa said the violence on London's streets was not coming from them.
Mr Da Costa had come to Britain from Portugal in 1996 and was a dad to a young boy.
His girlfriend is pregnant with his second child - a fundraising page was set up after his death to help with funeral and legal costs.