The bomb was discovered during construction work near the city's central train station.
Trains, trams and buses were halted or rerouted for the operation to dispose of the British 500-kilogramme bomb found more than 70 years after the war.
Police wrote on Twitter on Wednesday that the bomb was in a safe condition and there was not causing any immediate danger.
DW reporter Rebecca Ritters was at the scene in Berlin and said the discovery of unexploded bombs was not uncommon in Germany with more than 2,000 tonnes of bombs and live ammunition unearthed across the country every year.
Trains were prevented from stopping at the busy station from 10 a.m., and through traffic was shut down at 11:30 a.m. before experts began their work, German rail operator Deutsche Bahn said.
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Police said a number of WW2 bombs had found in this area earlier too.
The central station falls just inside the evacuation area, according to the BerlinerMorgenpost, and is a major stop for long-distance trains. Before the bomb disposal experts move in, police will go house to house to check the zone has been completely cleared. Berlin was reduced to ruins in 1945 and about 3000 unexploded bombs are believed to be still lying buried in the city.
Flights from Berlin's Tegel airport are not affected but passengers have been warned that public transport to the city's two airports - Tegel and Schoenefeld - would be disrupted.
"Residents are being asked to leave their homes due to the bomb from the World War being defused".
Berlin is set to hold a large-scale evacuation Friday to allow experts to defuse a 1,100-pound World War II explosive.