A major department store and a huge Christmas tree outside parliament were also set alight.
More than 200 fires were started in Athens on Monday, the fire department said.
As the violence raged, about 10,000 protesters from the Communist Party of Greece and the Coalition of the Left marched through Athens to protest against the killing of 15-year-old Alexandros Grigoropoulos in the traditionally left-wing Exarchia district on Saturday.
Alexis Tsipras, the coalition leader, said the teenager's shooting had resulted in "a spontaneous youthful uprising".
"The prime minister has a deep political responsibility. But instead of taking it, he is rejecting the ... resignations of the responsible ministers, he is adopting the version of an isolated incident and barricading himself behind broken storefronts," he said.
Barnaby Phillips, Al Jazeera's correspondent in Athens, said the government and the police appeared to have been caught on the back foot by the violence.
The centre-right government was already in trouble and clinging on to power with a very small majority, our correspondent explained.
Ministers had gone on television to apologise for the death of the boy as much as they were condemning the widespread looting and violence, he added.
Grigoropoulos's funeral will be held on Tuesday, and schools are to remain shut in mourning.
Two officers have been charged over the shooting - one with premeditated manslaughter and the illegal use of a weapon and the other as an accomplice.
|The funeral of Grigoropoulos will be held on Tuesday
They are due to appear before a court on Wednesday and both have been suspended - along with the Exarchia precinct police chief.
Panayiotis Stathis, a police spokesman, said 89 people had been arrested for attacks on police, vandalism and looting since the violence began.
Another 79 people had been detained for questioning over the riots in which dozens of police officers have been injured.
Small groups of youths continued to occupy university campuses in the centre of the capital, throwing stones and Molotov cocktails at police.
In Germany, more than 15 people occupied the Greek consulate in the heart of Berlin's downtown shopping district on Monday, hanging a banner and throwing down pamphlets to urge resistance against state force.
No violence was reported and the protesters walked out of the building peacefully, past police officers, eight hours later.
Demonstrations also took place in London and Nicosia in Cyprus.
Earlier on Monday, hundreds of students clashed with police in the northern Greek city of Thessaloniki.
Around 300 people threw fire bombs at riot police and attacked cars and shops as demonstrations spilled over into violence.
|Youths took over the Greek consulate in Berlin to protest the shooting [Reuters]
Two people were detained as police used tear gas against the rioters.
There were also clashes in the central city of Trikala, where dozens of youths broke off from a student demonstration and attacked banks, shops and cars on the city's main square.
The popularity of Karamanlis has been hit by the poor state of the country's economy and a number of scandals that saw three ministers leave government last year.
After the cabinet meeting on Monday, his government defended the handling of the unrest.
Prokopis Pavlopoulos, the Greek interior minister who offered to resign on Sunday, said the police action had been intended to "protect human life and property".
"The state machinery has protected more things than those that were threatened ... it is there to protect human life and everything else, without threatening democracy," the minister said.