The small groups of youths also tore down street signs, toppled garbage bins and set fire to debris on Wednesday.
Riot police were on the scene, but generally did not interfere.
School pupils, university students and left-wing organizations are holding protests in Greece's main cities in memory of 15-year-old Alexis Grigoropoulos, who was fatally shot by a police officer in 2008.
At the time, Grigoropoulos' death sparked days of youth unrest around Greece.
Greek police are already on alert over a two-day visit by Turkish President Recep Tayyip Erdogan starting on Thursday.
The officer who shot Grigoropoulos following a street row, Epaminondas Korkoneas, was in 2010 found guilty of culpable homicide and sentenced to life in prison for the killing.
At his trial, Korkoneas claimed he had fired warning shots to keep back youngsters who were hurling objects at him and his patrol partner.
One of his bullets deflected onto the boy's chest, killing him before he could be taken to hospital.
His patrol partner Vassilios Saraliotis was sentenced to 10 years for complicity, but was conditionally freed in 2011.