S-Bahn services running through the congested inner city section between Munich Central Station and Laim were also affected.
Deutsche Bahn (DB) confirmed in a press release that all services had returned to normal by 12.05 pm.
The fire services brought 80 vehicles into service to deal with the burning engine at a point on the tracks between Donnersberger Brücke and Hirschgarten.
While the cause of the fire remains unclear, a spokesperson for DB reported a technical failure, reports Focus.
The train in question was an intercity (IC) vehicle which had set off from Munich at 7am. Fire services evacuated people from the first three carriages into the rear carriage and then pulled the rear carriages back to the central station.