The two men, 21 and 22, were part of a group of three men police were looking for in connection with the death of the 23-year-old, a spokesman said on Sunday.
"They admitted that they had something to do with the case and were arrested," he said.
On Saturday at around 4:50 am, the 23-year-old and a companion were attacked by three other men in the Kaiserdamm U-Bahn station in western Berlin. While one man managed to flee, the 23-year-old was hit by a passing car after he ran from the station and attempted to cross the road.
Despite efforts by emergency personnel, he died on the scene.
Police did not release additional details about the two men now in custody, saying only that the case had been passed on to the Berlin homicide division.
Over the past few months, there have been a number of reports of brutal assaults in Berlin subway stations. The conservative Christian Democrats (CDU) have used the issue in their election campaign to cast doubt on the current government's record on security and law enforcement.
At Easter, a 29-year-old was severely injured by an 18-year-old man in the Friedrichshain station. That case has come to trial and a verdict is expected next week.