The travel plans of around 90,000 people were disrupted when an exclusion zone was thrown up around the shell, which was discovered in the north of Tokyo earlier this year.
A squad from the country's Ground Self-Defense Force piled sandbags on top of the shell before detonating it around noon.
A total of 150 train services, including 53 Shinkansen bullet-train services, were affected, a spokesman for East Japan Railway (JR East) said ahead of the operation, adding 90,000 people would be affected.
Despite massive redevelopment in the nearly 70 years since WWII, finds of unexploded ordinance are not uncommon in and around Japan's cities, which were heavily bombed by US forces.