Almost 450,000 people in the southern half of the city were affected when what is believed to have been a technical problem struck at an electrical substation.
Buildings were plunged into darkness at 7 am, said the Munich fire brigade. The power cut caused fire alarms to go off, sparking a stream of fake alerts to those with an automatic line to the emergency services.
The emergency services were called out to 50 genuine cases, some of which involved people stuck in lifts.
Parts of the city regained power within 15 minutes but others had to wait up to an hour until they were re-connected.
Large sections of the city's metro and suburban train networks stopped working, leaving around 10,000 commuters stranded on platforms en route to work. Cars and buses were also affected as traffic lights cut out.
The cause remains unconfirmed but experts have suggested that it could have been caused by a surge of electricity at the plant which caused it to break down temporarily.