Tagesspiegel reported that a fire service spokesman confirmed the negative test results from the Tropical Medicine Institute of the Virchow Clinic.
Emergency services had been deployed to the capital's Neukölln district on Monday night after a man showed symptoms of the Ebola virus.
The spokesman said that the man is an interpreter who has worked with refugees from Sierra Leone.
Police and fire services with full isolation gear were called to the scene just before 11 pm on Monday.
The street was closed off for around four hours while the man was loaded into an ambulance and the emergency services decontaminated the people who had come into contact with him.
His two flatmates were placed into quarantine and prevented from leaving the apartment.
Test results revealing whether the man is really suffering from the virus are expected later on Tuesday.