Around 200 residents evacuated their homes within a 100-meter (330-foot) radius of the 500-pound bomb, which was found last month at a construction site in Motoakasaka area of Minato ward, as soldiers worked on removing the device.
Japanese Self Defense Force members started to defuse the rusty ordnance, which was discovered 4.5-meters (15-feet) underground, at 9:13 am (00:13 GMT) and had safely removed it from the area by 10:18 am, local officials said.
The area was declared safe shortly afterwards, they added.
Tokyo was a target of intense US air raids near the end of the World War II and around 70 unexploded bombs are found in the capital every year, according to the local administrative office.