Witnesses said the shooting occurred around 9 p.m. when a small group of youths attacked a police patrol car. An officer fired three shots, hitting the youth in the chest.
Police issued a statement saying the patrol car, with two officers inside, was attacked by a group of 30 stone-throwing youths while patrolling the central district of Exarchia. According to the statement, the two officers left their car to confront the rioters.
"The two (police officers) maintain that they were attacked again and responded, with one firing a stun grenade and the other, by shooting three times, resulting in the fatal wounding of the minor," the statement said.
Two Greek TV stations said the young man who had been shot was rushed to a hospital, but died upon arrival.
The two officers and the local precinct commander have been suspended pending an investigation, the police statement said.
"The government expresses its profound regret over this incident. An inquiry on the circumstances of the death has already begun and, if the policemen are found to have been derelict in their duty, the punishment will be exemplary," Interior Minister Prokopis Pavlopoulos said in a statement.
News of the shooting enraged hundreds of youths in the area, who began rioting, attacking other police cars with stones and firebombs. Police responded by firing tear gas at the crowd, evacuating some restaurants in the area, and closing several streets to all traffic.
A few hours after the rioting began, the youths appeared to divide into at least three separate groups and there was a lull in the fighting.
Shortly after midnight, rioting resumed with some protesters marching through the city center and others fighting police nearby. Police fired tear gas, and rioters threw stones and firebombs.
In the northern city of Thessaloniki, dozens of youths attacked a police precinct in the city center and several others have blockaded a road.
At least one teenager was arrested, but no casualties were reported among the rioters or police.
Calls were posted on Web sites for more people to join the protests in the two main cities as well as the city of Iraklio on the island of Crete.