Residents of the capital of the northern state of Lower Saxony had been told to leave their homes in the early evening on Monday as a precaution on the discovery of the 250-kilogramme (550-pound) device.
Tweets less than an hour apart from the city hall reported the bomb defusal team starting work and then issuing the all-clear at 01:07 am.
The unearthing of World War II era bombs is a common occurrence in Hanover, home to some 500,000 people and one of dozens of cities the Allies targeted during the conflict.
The largest post-war evacuation happened in September 2017, following the discovery of a bomb weighing several tons near the Frankfurt university campus. More than 60,000 people were affected.
Around one in ten of the millions of bombs dropped over Germany during the war did not go off, according to experts cited by news weekly Der Spiegel.
On Monday evening, a second unexploded bomb in the western city Cologne was also defused, after 4,800 people were evacuated.