Police announced the measure at around 9.00am on Sunday after a Second World War bomb was found at a building site near the Jewish Museum on Lindenstrasse.
By the early evening, specialists had managed to defuse the two detonators of the American weapon, Berlin newspaper the Tagesspiegel reported.
Defusing the bomb took place much later than planned after the huge logistical effort of evacuating 11,000 inhabitants from the inner city Berlin neighbourhood.
Residents had already been informed of the evacuation on Saturday evening.
The Jewish Museum remained closed through the entirety of Sunday as the underground lines U6 and U12 were also blocked in sections.
Large bombs dropped on German urban centres during the Second World War are often still unearthed during building projects.
In Munich earlier this month, evacuations took place around the Deutsches Museum after a large bomb was found there. Due to complications, the bomb had to be taken from the site while still live.