Firefighters were called to the Parkweg bridge, which carries traffic from Treptow into Friedrichshain, at 4.25am on Thursday.
The cable duct is hard to get to suggesting it was a planned attack, a spokesman for the S-Bahn told The Local.
“The arsonists had to purposefully climb over fences and move the cover of the duct, which is made of concrete and quite heavy, to one side,” he said.
“If people are determined then of course they'll be able to break into such places, but it's not as if you don't have to make an effort.”
Traffic has been interrupted on the S41, S42, S47, S8, S85 and S9 lines between Ostkreuz and Neukölln and Baumschulenweg since the blaze. Around 30 buses have been deployed to provide a replacement service and additional staff are at stations to provide information.
GALLERY: Disruption in southeast Berlin after arsonists hit S-Bahn
“We hope most Berliners still got to their destination in reasonable time,” the S-Bahn spokesman said.
The S41 and S42 ring service is running, but there is no service between Ostkreuz and Südkreuz.
Connections to other U- and S-Bahn lines are available at all the other stations on the southern half of the Berlin ring and the S-Bahn operator is encouraging passengers to use the replacement buses only if there is no other way to reach their destination.
Parts of other S-Bahn lines are likely to experience a reduced service over the weekend as repair work continues.