Police said about 30 men and women broke through the main entrance during the afternoon.
The group hung a flag symbolising the Syrian resistance movement from one of the windows and spray-painted political slogans in Arabic and English on the front of the building, including one that read "Revolution and Freedom."
The Federal Foreign Office said the German government takes its responsibility to safeguard all diplomatic and consular representatives in Germany seriously.
"Attacks on embassies and consulates must be pursued with the utmost consistency," a statement read. Boris Ruge, the office's head of Middle East affairs, expressed his regret over the incident in a phone call to the Syrian ambassador.
The group also destroyed some of the furniture in the embassy office before being taken into custody by police. They did not resist arrest, and were later released. Police said all of those involved in the incident were of Syrian descent.
Syria's ambassador to Germany has filed charges, and police are investigating the group for disturbing the peace, property damage and trespassing. It is the second time activists have stormed the embassy since October of last year.
The violence in Syria has intensified in recent days, with reports of hundreds dead in the city of Homs on Friday. The United Nations estimates that at least 5,600 people have been killed since March in the Syrian government's violent crackdown on dissent.