After several days of rumours that the launch was imminent, Japan - one of the world's biggest gaming markets - joined the United States, Canada, Australia and more than 30 countries in Europe in playing the "augmented-reality" game by Nintendo Co Ltd in which players interact with virtual characters in the real world.
Junichi Masuda, head of development at Game Freak, and co-creator of the game, apologised in a video announcement on the Internet for keeping players waiting so long in the land where Pokemon was first born two decades ago.
"From today you can go out and find Pokemon to your heart's content," he said.
"We hope the game enables users to see the world in a new, fulfilling way. Obey the rules and have fun."
Initial attempts to download the game took some time, but before long players were starting to hunt and capture the monsters, which showed up even in ordinary offices.
"This game is just as I imagined it to be, it's really fun," said Toshinori Ishibashi, 18, who was seen playing the game near a Pokemon goods store in Tokyo Station.
"It's also a great reason to go outside, so I'm really enjoying it."
(Also see: Pokemon Go: How to Catch Pikachu)
The game was created by Nintendo, Niantic, and Pokemon Co. Nintendo owns a third of Pokemon Co, and both have undisclosed stakes in Niantic.
McDonald's Holdings Co Japan Ltd teamed up for the launch and said its nearly 3,000 shops across Japan would serve as spots where Pokemon can be battled or "trained" in the game - but added a very Japanese caveat.
"Ultimately, McDonald's is a restaurant," said a company spokesman. "We will call on players not to become a bother to customers who are eating."
The Japanese government on Thursday issued a safety warning, with the country's National Center for Incident Readiness and Strategy for Cybersecurity (NISC) giving nine instructions to users of the mobile game, ranging from advising them not to use their real names to warning about heat stroke in the muggy Japanese summer.
Nintendo shares climbed more than 4 percent in Tokyo trading on Friday, while shares of McDonald's Japan surged 7.2 percent.
© Thomson Reuters 2016