Both trains, mainly filled with school children, were directed into platform two of Utting station, at 7.50 am on Thursday, the Süddeutsche Zeitung reports.
The catastrophic accident was only avoided when the driver of the southbound train noticed the other train standing at the platform that he was headed towards pulled the emergency break. By the time the train came to a stop, only 40 metres reportedly separated the two locomotives.
Rail provider Bayerische Regiobahn (BRB) has made no official comment on the near miss. But, according to the SZ, the train dispatcher at Utting station was sacked immediately after the incident.
Utting on Amersee to the southwest of Munich. Google Maps
The trains were supposed to be directed past one another at the two platform station - on both sides of the station the line is only single track.
A spokesman for BRB praised the quick reactions of the driver, saying that he wanted to personally thank him in the coming days.
The track around Utting station was closed on Thursday as investigative teams looked into how the near collision could have come to pass. A bus replacement service was put in place.
The near misses comes shortly after the second anniversary of a horriffic collision between two regional trains not far away in Bad Aibling. Twelve people died in that crash and 89 were injured.