Police reported on Monday that the accident occurred on the S1 line between the stations Wittenau and Wilhelmsruh.
Police believe the two were on a section of the S-Bahn rails on a bridge when a train heading in the direction of Wannsee drove through and rolled over them.
The train driver told police that he heard a rumbling sound, and then stopped the train. He then found the two young men, already dead, after he got out of the train to figure out what had caused the noise.
Fresh graffiti was found in the area of the bridge where the teens had been, as well as several cans of paint and a backpack containing other graffiti paraphernalia.
According to Tagesspiegel, the victims were from Berlin and were already known to police as graffiti painters, as well as for other crimes.
A police helicopter was called to the spot in order to light up the scene while the bodies of the two were removed by the fire services.
The train was able to travel on from the scene of the incident after two hours. However, the 50 passengers on board the S1 train had to remain inside the carriage for the two hours while the bodies were being removed because it was too risky to have them exit out of the train and across the tracks in the dark.
The police investigation into the deaths of the teenagers is ongoing.
This is not the first train-related death to occur in recent weeks, according to Tagesspiegel. The body of a 22-year-old man, who had attempted to U-Bahn-surf, was discovered last weekend on the roof of a train as it entered Möckernbrücke station.
During the same night that the two teenagers were killed, another graffiti sprayer narrowly avoided being seriously hurt at Greifswalder Straße station, after climbing onto a parked goods wagon while attempting to evade police.