The attack, which caused no injuries or damage, followed a bombing at a Jewish cemetery and two assaults on Jews in the capital in recent weeks. Police offered a 3,000 euro (dlrs 2,700) reward for information leading to arrests.
The unknown assailant lobbed a Molotov cocktail over the synagogue's fence from an adjacent park Sunday night and fled, police said. The flaming bottle landed on the synagogue lawn "at a considerable distance" from the building, where a police guard stamped it out.
Police said were on the scene Monday investigating. The same synagogue was targeted in a vandalism attack in October 2000, when someone threw stones and broke two windows in the building in the western Kreuzberg district.
Police said they were considering both far-right extremism and the Middle East conflict as possible motives.
Germany's Central Council of Jews said the latest incident showed "that the spiral of violence against Jewish locations and people is escalating further also in Germany." It urged German politicians and law enforcement officials to combat the attacks.
Germany's interior minister this month asked state governments to review security arrangements for Jewish sites in the country after attacks on synagogues in France and Belgium.
Two weeks ago, two Berlin Jewish women suffered bruises in an assault by two young men of Arab appearance at a subway station. The victims ripped a Star of David necklace off the younger woman and hit her and her mother in the face before fleeing, police said.
Berlin police also are investigating an assault by a group of youths on two 21-year-old Orthodox Jews from New York last month. In March, a homemade explosive device blew up at the entrance to a Jewish cemetery in Berlin, shattering several windows. Police said they suspect neo-Nazis but no arrests have been made.