The worker confessed at the start of his trial last month that he had been playing a mobile phone game while on duty.
Michael Paul, 40, was found guilty of involuntary manslaughter over the February accident near the southern town of Bad Aibling, in which two commuter trains collided head-on at high speed.
Paul said he was playing Dungeon Hunter 5, a fantasy role-play game, and ended up setting the wrong train signals. Although he had a chance to prevent the head-on crash through an emergency call placed to the train drivers, he dialed the wrong number, said his lawyer.
"The accused is guilty of 12 counts of involuntary manslaughter and 85 counts of negligent bodily harm," presiding judge Erich Fuchs said as he read out the verdict following one of Germany's worst train crashes in decades.
As the trial opened, Paul had his lawyers read out his confession in which he admitted to negligence, but also addressed victims' relatives personally.
"I know that I cannot undo what has happened, even if I wish I could," he told them.
The accident was Germany's first fatal train crash since April 2012, when three people were killed and 13 injured in a collision between two regional trains in the western city of Offenbach.
The country's deadliest post-war rail accident happened in 1998 when a high-speed ICE train linking Munich and Hamburg derailed in the northern town of Eschede, killing 101 people and injuring 88.
Authorities said after the Bad Aibling disaster an investigation had ruled out a technical defect as the cause.