The Japanese city, considered a favorite to be chosen as host, prevailed over Istanbul in a second-round vote Saturday among IOC members gathered in Buenos Aires.
A third finalist, Madrid, was eliminated from consideration during the first round of voting.
Tokyo representatives had portrayed their city as the safe choice, a modern metropolis that had provided a successful
That might have resonated with IOC members who have dealt with reports of confusion and delay in Rio de Janeiro, the site of the upcoming 2016 Summer Games.
Madrid was seen as the least expensive option.
Istanbul would have provided an opportunity for the Olympic movement to gain more traction in the Islamic world.
The only hot-button issue for Tokyo was fallout from the Fukushima nuclear plant 150 miles away. Fukushima sustained major damage following a 9.0 earthquake and tsunami in March 2011.
"Let me assure you, the situation is under control," Japanese Prime Minister Shinzo Abe said. "It has never done and will never do any damage to Tokyo."
Japan also has a $4.5 billion reserve fund to cover Olympic cost contingencies.