The capital's government changed the regulations in order to enable violent hooligans to be banned from the trains for a year.
Three teenagers were the first to be barred from using the service after they threatened passengers with a starting pistol on the journey between Ostbahnhof and Warschauer Strasse.
Having been handed the ban, they could be charged with trespassing if they get on a train or even enter a train station in the next 12 months.
Until now those causing trouble on the trains could be removed, but not kept from S-Bahn property – once escorted off the train or out of the station by police, they were legally free to go back and get on the next one.
Free Democrat (FDP) state MP Klaus-Peter von Lüdeke joined other politicians in welcoming the new rule, but stressed the means had to be provided to enforce it.
“There must be enough security personnel on the train stations and in the trains to do this,” he told Die Welt newspaper.